def test_savetiff(self):
testfile = path.join(thisdir, 'coretestdata', 'testsave.tiff')
#create a few different data types
testb = ImageArray(np.zeros((4, 5), dtype=bool)) #bool
testb[0, :] = True
testui = ImageArray(np.arange(20).reshape(4, 5)) #int32
testi = ImageArray(np.copy(testui) - 10)
testf = ImageArray(np.linspace(-1, 1, 20).reshape(4, 5)) #float64
for im in [testb, testui, testi, testf]:
im['a'] = [1, 2, 3]
im['b'] = 'abc' #add some test metadata
im.filename = testfile
im.save()
n = ImageArray(testfile)
self.n = n
self.assertTrue(
all([n['a'][i] == im['a'][i] for i in range(len(n['a']))]))
self.assertTrue(n['b'] == im['b'])
self.assertTrue(
'ImageArray.dtype'
in n.metadata.keys()) #check the dtype metdata got added
self.assertTrue(im.dtype == n.dtype) #check the datatype
self.im = im
self.n = n
self.assertTrue(np.allclose(im, n)) #check the data
def setUp(self):
#random array shape 3,4
self.arr = np.array([[0.41674764, 0.66100043, 0.91755303, 0.33796703],
[0.06017535, 0.1440342, 0.34441777, 0.9915282],
[0.2984083, 0.9167951, 0.73820304, 0.7655299]])
self.imarr = ImageArray(np.copy(self.arr)) #ImageArray object
self.imarrfile = ImageArray(
os.path.join(thisdir, 'coretestdata/im1_annotated.png'))
def switch_index(self, saturation_end=True, saturation_value=True):
"""Given a stack of boolean masks representing a hystersis loop find the stack index of the saturation field for each pixel.
Take the final mask as all switched (or the first mask if saturation_end
is False). Work back through the masks taking the first time a pixel
switches as its coercive field (ie the last time it switches before
reaching saturation).
Elements that start switched at the lowest measured field or never
switch are given a zero index.
At the moment it's set up to expect masks to be false when the sample is saturated
at a high field
Keyword Arguments:
saturation_end(bool):
True if the last image is closest to the fully saturated state.
False if you want the first image
saturation_value(bool):
if True then a pixel value True means that switching has occured
(ie magnetic saturation would be all True)
Returns:
switch_ind: MxN ndarray of int
index that each pixel switches at
switch_progession: MxNx(P-1) ndarray of bool
stack of masks showing when each pixel saturates
"""
ms = self.clone
if not saturation_end:
ms = ms.reverse()
# arr1 = ms[0].astype(float) #find out whether True is at begin or end
# arr2 = ms[-1].astype(float)
# if np.average(arr1)>np.average(arr2): #OK so it's bright at the start
if not saturation_value:
self.imarray = np.invert(
ms.imarray) # Now it's bright (True) at end
switch_ind = np.zeros(ms[0].shape, dtype=int)
switch_prog = self.clone
switch_prog.imarray = np.zeros(self.shape, dtype=bool)
del switch_prog[-1]
for m in reversed(range(len(ms) - 1)): # go from saturation backwards
already_done = np.copy(switch_ind).astype(
dtype=bool) # only change switch_ind if it hasn't already
condition = np.logical_and(not ms[m], ms[m + 1])
condition = np.logical_and(condition, np.invert(already_done))
condition = [condition, np.logical_not(condition)]
choice = [np.ones(switch_ind.shape) * m,
switch_ind] # index or leave as is
switch_ind = np.select(condition, choice)
switch_prog[m] = already_done
if not saturation_end:
switch_ind = -switch_ind + len(self) - 1 # should check this!
switch_prog.reverse()
switch_ind = ImageArray(switch_ind.astype(int))
return switch_ind, switch_prog
def test_filename(self):
im = ImageArray(np.linspace(0, 1, 12).reshape(3, 4))
fpath = os.path.join(thisdir, 'coretestdata/im1_annotated.png')
self.assertTrue(os.path.normpath(self.imarrfile.filename)\
== os.path.normpath(fpath))
im = ImageArray(np.linspace(0, 1, 12).reshape(3, 4))
im['Loaded from']
im.filename
self.assertTrue(im.filename == '',
'{}, {}'.format(self.imarr.shape, im.filename))
def test_load_kwargs(self):
#metadata keyword arg
t = ImageArray(self.arr, metadata={'a': 5, 'b': 7})
self.assertTrue('a' in t.metadata.keys() and 'b' in t.metadata.keys())
self.assertTrue(t.metadata['a'] == 5)
#asfloat
t = ImageArray(np.arange(12).reshape(3, 4), asfloat=True)
self.assertTrue(t.dtype == np.float64, 'Initialising asfloat failed')
self.assertTrue('Loaded from' in t.metadata.keys(),
'Loaded from should always be in metadata')
def setUp(self):
self.a = ImageArray(join(thisdir,
'coretestdata/im2_noannotations.png'))
self.a1 = ImageArray(join(thisdir, 'coretestdata/im1_annotated.png'))
self.a2 = STXMImage(
join(thisdir, "..", "..", "..", "sample-data",
"Sample_Image_2017-10-15_100.hdf5"))
self.a3 = STXMImage(
join(thisdir, "..", "..", "..", "sample-data",
"Sample_Image_2017-10-15_101.hdf5"))
def test_save(self):
testfile = path.join(thisdir, 'coretestdata', 'testsave.png')
keys = self.imarr.keys()
self.imarr.save(filename=testfile)
load = ImageArray(testfile, asfloat=True)
#del load["Loaded from"]
self.assertTrue(all([k in keys for k in load.keys()]),
'problem saving metadata')
self.assertTrue(np.allclose(self.imarr, load, atol=0.001))
os.remove(testfile) #tidy up
def test_save(self):
testfile=path.join(thisdir,'coretestdata','testsave')
ext = ['.png', '.npy']
keys=self.imarr.keys()
for e in ext:
self.imarr.save(filename=testfile+e)
load=ImageArray(testfile+e)
self.assertTrue(all([k in load.keys() for k in keys]), 'problem saving metadata {} {}'.format(list(load.keys()),e))
if e=='.npy':
#tolerance is really poor for png whcih savees in 8bit format
self.assertTrue(np.allclose(self.imarr, load),
'data not the same for extension {}'.format(e))
os.remove(testfile+e) #tidy up
def test_save(self):
testfile = path.join(thisdir, 'coretestdata', 'testsave')
ext = ['.png', '.npy']
keys = self.imarr.keys()
for e in ext:
self.imarr.save(filename=testfile + e)
load = ImageArray(testfile + e)
self.assertTrue(all([k in keys for k in load.keys()]),
'problem saving metadata')
if e == '.npy':
#tolerance is really poor for png whcih savees in 8bit format
self.assertTrue(np.allclose(self.imarr, load),
'data not the same for extension {}'.format(e))
os.remove(testfile + e) #tidy up
def test_load_from_png(self):
subpath = os.path.join("coretestdata", "im1_annotated.png")
fpath = os.path.join(thisdir, subpath)
anim = ImageArray(fpath)
self.assertTrue(
os.path.normpath(anim.metadata['Loaded from']) == os.path.normpath(
fpath))
cwd = os.getcwd()
os.chdir(thisdir)
anim = ImageArray(subpath)
#check full path is in loaded from metadata
self.assertTrue(
os.path.normpath(
anim.metadata['Loaded from']) == os.path.normpath(fpath),
'Full path not in metadata: {}'.format(anim["Loaded from"]))
os.chdir(cwd)
def setUp(self):
#random array shape 3,4
self.arr = np.array([[ 0.41674764, 0.66100043, 0.91755303, 0.33796703],
[ 0.06017535, 0.1440342 , 0.34441777, 0.9915282 ],
[ 0.2984083 , 0.9167951 , 0.73820304, 0.7655299 ]])
self.imarr = ImageArray(np.copy(self.arr)) #ImageArray object
self.imarrfile = ImageArray(os.path.join(thisdir, 'coretestdata/im1_annotated.png'))
def test_load_from_ImageFile(self):
#uses the ImageFile.im attribute to set up ImageArray. Memory overlaps
imfi = ImageFile(self.arr)
imarr = ImageArray(imfi)
self.assertTrue(np.array_equal(imarr, imfi.image),
'Initialising from ImageFile failed')
self.assertTrue(shares_memory(imarr, imfi.image))
class FuncsTest(unittest.TestCase):
def setUp(self):
self.a=ImageArray(join(thisdir,'coretestdata/im2_noannotations.png'))
self.a1=ImageArray(join(thisdir,'coretestdata/im1_annotated.png'))
self.a2=STXMImage(join(thisdir,"..","..","..","sample-data","Sample_Image_2017-10-15_100.hdf5"))
self.a3=STXMImage(join(thisdir,"..","..","..","sample-data","Sample_Image_2017-10-15_101.hdf5"))
def test_imagefile_ops(self):
self.a2.gridimage()
self.a3.gridimage()
self.a2.crop(5,-15,5,-5,_=True)
self.a3.crop(5,-15,5,-5,_=True)
self.b=self.a2//self.a3
self.assertEqual(self.b.shape,(90,80),"Failure to crop image correctly.")
self.assertGreater(self.b.max(),0.047,"XMCD Ratio calculation failed")
self.assertLess(self.b.min(),-0.05,"XMCD Ratio calculation failed")
self.b.normalise()
self.assertEqual(self.b.max(),1.0,"Normalise Image failed")
self.assertEqual(self.b.min(),-1.0,"Normalise Image failed")
self.profile=self.b.profile_line((0,0),(100,100))
self.profile.plot()
self.b.mask=self.a2.image>25E3
self.hist=self.b.hist(bins=200)
self.hist.column_headers=["XMCD Signal","Frequency"]
self.hist.labels=None
g1=LorentzianModel(prefix="g1_")
g2=LorentzianModel(prefix="g2_")
params=g1.make_params()
params.update(g2.make_params())
double_peak=g1+g2
g1=np.argmax(self.hist.y[:100]) # Location of first peak
g2=np.argmax(self.hist.y[100:])+100
for k, p in zip(params,[0.25,self.hist.x[g1],self.hist.y[g1]/np.sqrt(2),0.5,self.hist.y[g1],
0.25,self.hist.x[g2],self.hist.y[g2]/np.sqrt(2),0.5,self.hist.y[g2]]):
params[k].value=p
print(g1,g2,params)
self.res=self.hist.lmfit(double_peak,p0=params,output="report")
self.hist.add_column(self.res.init_fit,header="Initial Fit")
self.hist.add_column(self.res.best_fit,header="Best Fit")
self.hist.setas="xyyy"
self.hist.plot(fmt=["b+","b--","r-"])
plt.close("all")
#self.b.adnewjust_contrast((0.1,0.9),percent=True)z
def test_funcs(self):
b=self.a.translate((2.5,3))
self.c=b.correct_drift(ref=self.a)
self.d=b.align(self.a,method="scharr")
tv=np.array(self.d["tvec"])*10
cd=np.array(self.c["correct_drift"])*10
shift=np.array([25,30])
d1=mag(cd-shift)
d2=mag(tv-shift)
self.assertLess(d1,1.5,"Drift Correct off by more than 0.1 pxiels.")
self.assertLess(d2,1.5,"Scharr Alignment off by more than 0.1 pxiels.")
def test_load_from_array(self):
#from array
self.assertTrue(np.array_equal(self.imarr, self.arr))
#int type
imarr = ImageArray(np.arange(12, dtype="int32").reshape(3, 4))
self.assertTrue(
imarr.dtype == np.dtype('int32'),
"Failed to set correct dtype - actual dtype={}".format(
imarr.dtype))
class FuncsTest(unittest.TestCase):
def setUp(self):
self.a = ImageArray(join(thisdir,
'coretestdata/im2_noannotations.png'))
self.a1 = ImageArray(join(thisdir, 'coretestdata/im1_annotated.png'))
def test_funcs(self):
b = self.a.translate((2.5, 3))
c = b.correct_drift(ref=self.a)
def test_user_attributes(self):
self.imarr.abc = 'new att'
self.assertTrue(hasattr(self.imarr, 'abc'))
t = ImageArray(self.imarr)
self.assertTrue(hasattr(t, 'abc'), 'problem copying new attributes')
t = self.imarr.view(
ImageArray) #check array_finalize copies attribute over
self.assertTrue(hasattr(t, 'abc'))
t = self.imarr * np.random.random(self.imarr.shape)
self.assertTrue(isinstance(t, ImageArray), 'problem with ufuncs')
self.assertTrue(hasattr(t, 'abc'), "Ufunc lost attribute!")
def test_other_funcs(self):
"""test imagefuncs add ons. the functions themselves are not checked
and should include a few examples in the doc strings for testing"""
self.assertTrue(hasattr(self.imarr, 'do_nothing'),
'imagefuncs not being added to dir')
self.assertTrue(hasattr(self.imarr, 'img_as_float'),
'skimage funcs not being added to dir')
im = self.imarr.do_nothing() #see if it can run
self.assertTrue(np.allclose(im, self.imarr), 'imagefuncs not working')
self.assertFalse(shares_memory(im, self.imarr),
'imagefunc failed to clone')
im0 = ImageArray(np.linspace(0, 1, 12).reshape(3, 4))
im1 = im0.clone * 5
im2 = im1.rescale_intensity() #test skimage
self.assertTrue(np.allclose(im2, im0), 'skimage func failed')
self.assertFalse(shares_memory(im2, im1), 'skimage failed to clone')
im3 = im1.exposure__rescale_intensity() #test call with module name
self.assertTrue(np.allclose(im3, im0),
'skimage call with module name failed')
def test_load_1d_data(self):
t = ImageArray(np.arange(10) / 10.0)
self.assertTrue(len(t.shape) == 2) #converts to 2d
def test_load_from_list(self):
t = ImageArray([[1, 3], [3, 2], [4, 3]])
self.assertTrue(np.array_equal(t, np.array([[1, 3], [3, 2], [4, 3]])),
'Initialising from list failed')
def test_load_from_ImageArray(self):
#from ImageArray
t = ImageArray(self.imarr)
self.assertTrue(shares_memory(self.imarr, t),
'no overlap on creating ImageArray from ImageArray')
class ImageArrayTest(unittest.TestCase):
def setUp(self):
#random array shape 3,4
self.arr = np.array([[ 0.41674764, 0.66100043, 0.91755303, 0.33796703],
[ 0.06017535, 0.1440342 , 0.34441777, 0.9915282 ],
[ 0.2984083 , 0.9167951 , 0.73820304, 0.7655299 ]])
self.imarr = ImageArray(np.copy(self.arr)) #ImageArray object
self.imarrfile = ImageArray(os.path.join(thisdir, 'coretestdata/im1_annotated.png'))
#ImageArray object from file
#####test loading with different datatypes ####
def test_load_from_array(self):
#from array
self.assertTrue(np.array_equal(self.imarr,self.arr))
#int type
imarr = ImageArray(np.arange(12,dtype="int32").reshape(3,4))
self.assertTrue(imarr.dtype==np.dtype('int32'),"Failed to set correct dtype - actual dtype={}".format(imarr.dtype))
def test_load_from_ImageArray(self):
#from ImageArray
t = ImageArray(self.imarr)
self.assertTrue(shares_memory(self.imarr, t), 'no overlap on creating ImageArray from ImageArray')
def test_load_from_png(self):
subpath = os.path.join("coretestdata","im1_annotated.png")
fpath = os.path.join(thisdir, subpath)
anim=ImageArray(fpath)
self.assertTrue(os.path.normpath(anim.metadata['Loaded from']) == os.path.normpath(fpath))
cwd = os.getcwd()
os.chdir(thisdir)
anim = ImageArray(subpath)
#check full path is in loaded from metadata
self.assertTrue(os.path.normpath(anim.metadata['Loaded from']) == os.path.normpath(fpath), 'Full path not in metadata: {}'.format(anim["Loaded from"]))
os.chdir(cwd)
def test_load_from_ImageFile(self):
#uses the ImageFile.im attribute to set up ImageArray. Memory overlaps
pass
# imfi = ImageFile(self.arr)
# imarr = ImageArray(imfi)
# self.assertTrue(np.array_equal(imarr, imfi.image), 'Initialising from ImageFile failed')
# self.assertTrue(shares_memory(imarr, imfi.image))
def test_load_from_list(self):
t=ImageArray([[1,3],[3,2],[4,3]])
self.assertTrue(np.array_equal(t, np.array([[1,3],[3,2],[4,3]])), 'Initialising from list failed')
def test_load_1d_data(self):
t=ImageArray(np.arange(10)/10.0)
self.assertTrue(len(t.shape)==2) #converts to 2d
def test_load_no_args(self):
#Should be a 2d empty array
t=ImageArray()
self.assertTrue(len(t.shape)==2)
self.assertTrue(t.size==0)
def test_load_bad_data(self):
def testload(arg):
ImageArray(arg)
#dictionary
self.assertRaises(ValueError, testload, {'a':1})
#3d numpy array
self.assertRaises(ValueError, testload, np.arange(27).reshape(3,3,3))
#bad filename
self.assertRaises(ValueError, testload, 'sillyfile.xyz')
def test_load_kwargs(self):
#metadata keyword arg
t=ImageArray(self.arr, metadata={'a':5, 'b':7})
self.assertTrue('a' in t.metadata.keys() and 'b' in t.metadata.keys())
self.assertTrue(t.metadata['a']==5)
#asfloat
t=ImageArray(np.arange(12).reshape(3,4), asfloat=True)
self.assertTrue(t.dtype == np.float64, 'Initialising asfloat failed')
self.assertTrue('Loaded from' in t.metadata.keys(), 'Loaded from should always be in metadata')
#####test attributes ##
def test_filename(self):
im = ImageArray(np.linspace(0,1,12).reshape(3,4))
fpath = os.path.join(thisdir, 'coretestdata/im1_annotated.png')
self.assertTrue(os.path.normpath(self.imarrfile.filename)\
== os.path.normpath(fpath))
im = ImageArray(np.linspace(0,1,12).reshape(3,4))
im['Loaded from']
im.filename
self.assertTrue(im.filename == '', '{}, {}'.format(self.imarr.shape, im.filename))
def test_clone(self):
self.imarr['abc'] = 123 #add some metadata
self.imarr['nested'] = [1,2,3] #add some nested metadata to check deepcopy
self.imarr.userxyz = 123 #add a user attribute
c = self.imarr.clone
self.assertTrue(isinstance(c,ImageArray), 'Clone not ImageArray')
self.assertTrue(np.array_equal(c,self.imarr),'Clone not replicating elements')
self.assertTrue(all([k in c.metadata.keys() for k in \
self.imarr.metadata.keys()]), 'Clone not replicating metadata')
self.assertFalse(shares_memory(c, self.imarr), 'memory overlap on clone') #formal check
self.imarr['bcd'] = 234
self.assertTrue('bcd' not in c.metadata.keys(), 'memory overlap for metadata on clone')
self.imarr['nested'][0] = 2
self.assertTrue(self.imarr['nested'][0] != c['nested'][0], 'deepcopy not working on metadata')
self.assertTrue(c.userxyz == 123)
c.userxyz = 234
self.assertTrue(c.userxyz != self.imarr.userxyz)
def test_metadata(self):
self.assertTrue(isinstance(self.imarr.metadata,typeHintedDict))
self.imarr['testmeta']='abc'
self.assertTrue(self.imarr['testmeta']=='abc', 'Couldn\'t change metadata')
del(self.imarr['testmeta'])
self.assertTrue('testmeta' not in self.imarr.keys(),'Couldn\'t delete metadata')
#bad data
def test(imarr):
imarr.metadata=(1,2,3)
self.assertRaises(TypeError, test, self.imarr) #check it won't let you do this
### test numpy like creation behaviour #
def test_user_attributes(self):
self.imarr.abc = 'new att'
self.assertTrue(hasattr(self.imarr, 'abc'))
t = ImageArray(self.imarr)
self.assertTrue(hasattr(t, 'abc'), 'problem copying new attributes')
t = self.imarr.view(ImageArray) #check array_finalize copies attribute over
self.assertTrue(hasattr(t, 'abc'))
t = self.imarr * np.random.random(self.imarr.shape)
self.assertTrue(isinstance(t, ImageArray), 'problem with ufuncs')
self.assertTrue(hasattr(t, 'abc'),"Ufunc lost attribute!")
##### test functionality ##
def test_save(self):
testfile=path.join(thisdir,'coretestdata','testsave')
ext = ['.png', '.npy']
keys=self.imarr.keys()
for e in ext:
self.imarr.save(filename=testfile+e)
load=ImageArray(testfile+e)
self.assertTrue(all([k in load.keys() for k in keys]), 'problem saving metadata {} {}'.format(list(load.keys()),e))
if e=='.npy':
#tolerance is really poor for png whcih savees in 8bit format
self.assertTrue(np.allclose(self.imarr, load),
'data not the same for extension {}'.format(e))
os.remove(testfile+e) #tidy up
def test_savetiff(self):
testfile=path.join(thisdir,'coretestdata','testsave.tiff')
#create a few different data types
testb = ImageArray(np.zeros((4,5), dtype=bool)) #bool
testb[0,:]=True
testui = ImageArray(np.arange(20).reshape(4,5)) #int32
testi = ImageArray(np.copy(testui)-10)
testf = ImageArray(np.linspace(-1,1,20).reshape(4,5)) #float64
for im in [testb, testui, testi, testf]:
im['a']=[1,2,3]
im['b']='abc' #add some test metadata
im.filename=testfile
im.save()
n = ImageArray(testfile)
self.n=n
self.assertTrue(all([n['a'][i]==im['a'][i] for i in range(len(n['a']))]))
self.assertTrue(n['b']==im['b'])
self.assertTrue('ImageArray.dtype' in n.metadata.keys()) #check the dtype metdata got added
self.assertTrue(im.dtype==n.dtype) #check the datatype
self.assertTrue(np.allclose(im, n)) #check the data
def test_max_box(self):
s=self.imarr.shape
self.assertTrue(self.imarr.max_box==(0,s[1],0,s[0]))
def test_crop(self):
c=self.imarr.crop((1,3,1,4),copy=True)
self.assertTrue(np.array_equal(c,self.imarr[1:4,1:3]),'crop didn\'t work')
self.assertFalse(shares_memory(c,self.imarr), 'crop copy failed')
c2=self.imarr.crop(1,3,1,4,copy=True)
self.assertTrue(np.array_equal(c2,c),'crop with seperate arguments didn\'t work')
c3 = self.imarr.crop(box=(1,3,1,4), copy=False)
self.assertTrue(np.array_equal(c3,c), 'crop with no arguments failed')
self.assertTrue(shares_memory(self.imarr, c3), 'crop with no copy failed')
def test_asint(self):
ui = self.imarr.asint()
self.assertTrue(ui.dtype==np.uint16)
intarr = np.array([[27312, 43319, 60132, 22149],
[ 3944, 9439, 22571, 64980],
[19556, 60082, 48378, 50169]], dtype=np.uint16)
self.assertTrue(np.array_equal(ui,intarr))
def test_other_funcs(self):
"""test imagefuncs add ons. the functions themselves are not checked
and should include a few examples in the doc strings for testing"""
self.assertTrue(hasattr(self.imarr,'do_nothing'), 'imagefuncs not being added to dir')
self.assertTrue(hasattr(self.imarr,'img_as_float'), 'skimage funcs not being added to dir')
im = self.imarr.do_nothing() #see if it can run
self.assertTrue(np.allclose(im, self.imarr), 'imagefuncs not working')
self.assertFalse(shares_memory(im, self.imarr), 'imagefunc failed to clone')
im0 = ImageArray(np.linspace(0,1,12).reshape(3,4))
im1 = im0.clone * 5
im2 = im1.rescale_intensity() #test skimage
self.assertTrue(np.allclose(im2, im0), 'skimage func failed')
self.assertFalse(shares_memory(im2, im1), 'skimage failed to clone')
im3 = im1.exposure__rescale_intensity() #test call with module name
self.assertTrue(np.allclose(im3, im0), 'skimage call with module name failed')
def index_to_field(self, index_map):
"""Convert an image of index values into an image of field values"""
fieldvals = np.take(self.fields, index_map)
return ImageArray(fieldvals)
def setUp(self):
self.a = ImageArray(join(thisdir,
'coretestdata/im2_noannotations.png'))
self.a1 = ImageArray(join(thisdir, 'coretestdata/im1_annotated.png'))
def testload(arg):
ImageArray(arg)
def test_load_no_args(self):
#Should be a 2d empty array
t = ImageArray()
self.assertTrue(len(t.shape) == 2)
self.assertTrue(t.size == 0)
def _load_ImageArray(f, **kargs):
"""Simple meothd to load an image array."""
kargs.pop("img_num", None)
return ImageArray(f, **kargs)
class ImageArrayTest(unittest.TestCase):
def setUp(self):
#random array shape 3,4
self.arr = np.array([[0.41674764, 0.66100043, 0.91755303, 0.33796703],
[0.06017535, 0.1440342, 0.34441777, 0.9915282],
[0.2984083, 0.9167951, 0.73820304, 0.7655299]])
self.imarr = ImageArray(np.copy(self.arr)) #ImageArray object
self.imarrfile = ImageArray(
os.path.join(thisdir, 'coretestdata/im1_annotated.png'))
#ImageArray object from file
#####test loading with different datatypes ####
def test_load_from_array(self):
#from array
self.assertTrue(np.array_equal(self.imarr, self.arr))
#int type
imarr = ImageArray(np.arange(12, dtype="int32").reshape(3, 4))
self.assertTrue(
imarr.dtype == np.dtype('int32'),
"Failed to set correct dtype - actual dtype={}".format(
imarr.dtype))
def test_load_from_ImageArray(self):
#from ImageArray
t = ImageArray(self.imarr)
self.assertTrue(shares_memory(self.imarr, t),
'no overlap on creating ImageArray from ImageArray')
def test_load_from_png(self):
subpath = os.path.join("coretestdata", "im1_annotated.png")
fpath = os.path.join(thisdir, subpath)
anim = ImageArray(fpath)
self.assertTrue(
os.path.normpath(anim.metadata['Loaded from']) == os.path.normpath(
fpath))
cwd = os.getcwd()
os.chdir(thisdir)
anim = ImageArray(subpath)
#check full path is in loaded from metadata
self.assertTrue(
os.path.normpath(
anim.metadata['Loaded from']) == os.path.normpath(fpath),
'Full path not in metadata: {}'.format(anim["Loaded from"]))
os.chdir(cwd)
def test_load_from_ImageFile(self):
#uses the ImageFile.im attribute to set up ImageArray. Memory overlaps
pass
# imfi = ImageFile(self.arr)
# imarr = ImageArray(imfi)
# self.assertTrue(np.array_equal(imarr, imfi.image), 'Initialising from ImageFile failed')
# self.assertTrue(shares_memory(imarr, imfi.image))
def test_load_from_list(self):
t = ImageArray([[1, 3], [3, 2], [4, 3]])
self.assertTrue(np.array_equal(t, np.array([[1, 3], [3, 2], [4, 3]])),
'Initialising from list failed')
def test_load_1d_data(self):
t = ImageArray(np.arange(10) / 10.0)
self.assertTrue(len(t.shape) == 2) #converts to 2d
def test_load_no_args(self):
#Should be a 2d empty array
t = ImageArray()
self.assertTrue(len(t.shape) == 2)
self.assertTrue(t.size == 0)
def test_load_bad_data(self):
def testload(arg):
ImageArray(arg)
#dictionary
self.assertRaises(ValueError, testload, {'a': 1})
#3d numpy array
self.assertRaises(ValueError, testload, np.arange(27).reshape(3, 3, 3))
#bad filename
self.assertRaises(ValueError, testload, 'sillyfile.xyz')
def test_load_kwargs(self):
#metadata keyword arg
t = ImageArray(self.arr, metadata={'a': 5, 'b': 7})
self.assertTrue('a' in t.metadata.keys() and 'b' in t.metadata.keys())
self.assertTrue(t.metadata['a'] == 5)
#asfloat
t = ImageArray(np.arange(12).reshape(3, 4), asfloat=True)
self.assertTrue(t.dtype == np.float64, 'Initialising asfloat failed')
self.assertTrue('Loaded from' in t.metadata.keys(),
'Loaded from should always be in metadata')
#####test attributes ##
def test_filename(self):
im = ImageArray(np.linspace(0, 1, 12).reshape(3, 4))
fpath = os.path.join(thisdir, 'coretestdata/im1_annotated.png')
self.assertTrue(os.path.normpath(self.imarrfile.filename)\
== os.path.normpath(fpath))
im = ImageArray(np.linspace(0, 1, 12).reshape(3, 4))
im['Loaded from']
im.filename
self.assertTrue(im.filename == '',
'{}, {}'.format(self.imarr.shape, im.filename))
def test_clone(self):
self.imarr['abc'] = 123 #add some metadata
self.imarr['nested'] = [1, 2,
3] #add some nested metadata to check deepcopy
self.imarr.userxyz = 123 #add a user attribute
c = self.imarr.clone
self.assertTrue(isinstance(c, ImageArray), 'Clone not ImageArray')
self.assertTrue(np.array_equal(c, self.imarr),
'Clone not replicating elements')
self.assertTrue(all([k in c.metadata.keys() for k in \
self.imarr.metadata.keys()]), 'Clone not replicating metadata')
self.assertFalse(shares_memory(c, self.imarr),
'memory overlap on clone') #formal check
self.imarr['bcd'] = 234
self.assertTrue('bcd' not in c.metadata.keys(),
'memory overlap for metadata on clone')
self.imarr['nested'][0] = 2
self.assertTrue(self.imarr['nested'][0] != c['nested'][0],
'deepcopy not working on metadata')
self.assertTrue(c.userxyz == 123)
c.userxyz = 234
self.assertTrue(c.userxyz != self.imarr.userxyz)
def test_metadata(self):
self.assertTrue(isinstance(self.imarr.metadata, typeHintedDict))
self.imarr['testmeta'] = 'abc'
self.assertTrue(self.imarr['testmeta'] == 'abc',
'Couldn\'t change metadata')
del (self.imarr['testmeta'])
self.assertTrue('testmeta' not in self.imarr.keys(),
'Couldn\'t delete metadata')
#bad data
def test(imarr):
imarr.metadata = (1, 2, 3)
self.assertRaises(TypeError, test,
self.imarr) #check it won't let you do this
### test numpy like creation behaviour #
def test_user_attributes(self):
self.imarr.abc = 'new att'
self.assertTrue(hasattr(self.imarr, 'abc'))
t = ImageArray(self.imarr)
self.assertTrue(hasattr(t, 'abc'), 'problem copying new attributes')
t = self.imarr.view(
ImageArray) #check array_finalize copies attribute over
self.assertTrue(hasattr(t, 'abc'))
t = self.imarr * np.random.random(self.imarr.shape)
self.assertTrue(isinstance(t, ImageArray), 'problem with ufuncs')
self.assertTrue(hasattr(t, 'abc'), "Ufunc lost attribute!")
##### test functionality ##
def test_save(self):
testfile = path.join(thisdir, 'coretestdata', 'testsave')
ext = ['.png', '.npy']
keys = self.imarr.keys()
for e in ext:
self.imarr.save(filename=testfile + e)
load = ImageArray(testfile + e)
self.assertTrue(all([k in keys for k in load.keys()]),
'problem saving metadata')
if e == '.npy':
#tolerance is really poor for png whcih savees in 8bit format
self.assertTrue(np.allclose(self.imarr, load),
'data not the same for extension {}'.format(e))
os.remove(testfile + e) #tidy up
def test_savetiff(self):
testfile = path.join(thisdir, 'coretestdata', 'testsave.tiff')
#create a few different data types
testb = ImageArray(np.zeros((4, 5), dtype=bool)) #bool
testb[0, :] = True
testui = ImageArray(np.arange(20).reshape(4, 5)) #int32
testi = ImageArray(np.copy(testui) - 10)
testf = ImageArray(np.linspace(-1, 1, 20).reshape(4, 5)) #float64
for im in [testb, testui, testi, testf]:
im['a'] = [1, 2, 3]
im['b'] = 'abc' #add some test metadata
im.filename = testfile
im.save()
n = ImageArray(testfile)
self.n = n
self.assertTrue(
all([n['a'][i] == im['a'][i] for i in range(len(n['a']))]))
self.assertTrue(n['b'] == im['b'])
self.assertTrue(
'ImageArray.dtype'
in n.metadata.keys()) #check the dtype metdata got added
self.assertTrue(im.dtype == n.dtype) #check the datatype
self.assertTrue(np.allclose(im, n)) #check the data
def test_max_box(self):
s = self.imarr.shape
self.assertTrue(self.imarr.max_box == (0, s[1], 0, s[0]))
def test_crop(self):
c = self.imarr.crop((1, 3, 1, 4), copy=True)
self.assertTrue(np.array_equal(c, self.imarr[1:4, 1:3]),
'crop didn\'t work')
self.assertFalse(shares_memory(c, self.imarr), 'crop copy failed')
c2 = self.imarr.crop(1, 3, 1, 4, copy=True)
self.assertTrue(np.array_equal(c2, c),
'crop with seperate arguments didn\'t work')
c3 = self.imarr.crop(box=(1, 3, 1, 4), copy=False)
self.assertTrue(np.array_equal(c3, c), 'crop with no arguments failed')
self.assertTrue(shares_memory(self.imarr, c3),
'crop with no copy failed')
def test_asint(self):
ui = self.imarr.asint()
self.assertTrue(ui.dtype == np.uint16)
intarr = np.array(
[[27312, 43319, 60132, 22149], [3944, 9439, 22571, 64980],
[19556, 60082, 48378, 50169]],
dtype=np.uint16)
self.assertTrue(np.array_equal(ui, intarr))
def test_other_funcs(self):
"""test imagefuncs add ons. the functions themselves are not checked
and should include a few examples in the doc strings for testing"""
self.assertTrue(hasattr(self.imarr, 'do_nothing'),
'imagefuncs not being added to dir')
self.assertTrue(hasattr(self.imarr, 'img_as_float'),
'skimage funcs not being added to dir')
im = self.imarr.do_nothing() #see if it can run
self.assertTrue(np.allclose(im, self.imarr), 'imagefuncs not working')
self.assertFalse(shares_memory(im, self.imarr),
'imagefunc failed to clone')
im0 = ImageArray(np.linspace(0, 1, 12).reshape(3, 4))
im1 = im0.clone * 5
im2 = im1.rescale_intensity() #test skimage
self.assertTrue(np.allclose(im2, im0), 'skimage func failed')
self.assertFalse(shares_memory(im2, im1), 'skimage failed to clone')
im3 = im1.exposure__rescale_intensity() #test call with module name
self.assertTrue(np.allclose(im3, im0),
'skimage call with module name failed')
def setUp(self):
self.a=ImageArray(join(thisdir,'coretestdata/im2_noannotations.png'))
self.a1=ImageArray(join(thisdir,'coretestdata/im1_annotated.png'))
self.a2=STXMImage(join(thisdir,"..","..","..","sample-data","Sample_Image_2017-10-15_100.hdf5"))
self.a3=STXMImage(join(thisdir,"..","..","..","sample-data","Sample_Image_2017-10-15_101.hdf5"))
class FuncsTest(unittest.TestCase):
def setUp(self):
self.a=ImageArray(join(thisdir,'coretestdata/im2_noannotations.png'))
self.a1=ImageArray(join(thisdir,'coretestdata/im1_annotated.png'))
self.a2=STXMImage(join(thisdir,"..","..","..","sample-data","Sample_Image_2017-10-15_100.hdf5"))
self.a3=STXMImage(join(thisdir,"..","..","..","sample-data","Sample_Image_2017-10-15_101.hdf5"))
def test_imagefile_ops(self):
self.a2.gridimage()
self.a3.gridimage()
self.a2.crop(5,-15,5,-5,_=True)
self.a3.crop(5,-15,5,-5,_=True)
self.b=self.a2//self.a3
self.assertEqual(self.b.shape,(90,80),"Failure to crop image correctly.")
self.assertGreater(self.b.max(),0.047,"XMCD Ratio calculation failed")
self.assertLess(self.b.min(),-0.05,"XMCD Ratio calculation failed")
self.b.normalise()
self.assertEqual(self.b.max(),1.0,"Normalise Image failed")
self.assertEqual(self.b.min(),-1.0,"Normalise Image failed")
self.profile=self.b.profile_line((0,0),(100,100))
self.profile.plot()
self.b.mask=self.a2.image>25E3
self.hist=self.b.hist(bins=200)
self.hist.column_headers=["XMCD Signal","Frequency"]
self.hist.labels=None
g1=LorentzianModel(prefix="g1_")
g2=LorentzianModel(prefix="g2_")
params=g1.make_params()
params.update(g2.make_params())
double_peak=g1+g2
g1=np.argmax(self.hist.y[:100]) # Location of first peak
g2=np.argmax(self.hist.y[100:])+100
for k, p in zip(params,[0.25,self.hist.x[g1],self.hist.y[g1]/np.sqrt(2),0.5,self.hist.y[g1],
0.25,self.hist.x[g2],self.hist.y[g2]/np.sqrt(2),0.5,self.hist.y[g2]]):
params[k].value=p
print(g1,g2,params)
self.res=self.hist.lmfit(double_peak,p0=params,output="report")
self.hist.add_column(self.res.init_fit,header="Initial Fit")
self.hist.add_column(self.res.best_fit,header="Best Fit")
self.hist.setas="xyyy"
self.hist.plot(fmt=["b+","b--","r-"])
plt.close("all")
#self.b.adnewjust_contrast((0.1,0.9),percent=True)z
def test_funcs(self):
b=self.a.translate((2.5,3))
self.c=b.correct_drift(ref=self.a)
self.d=b.align(self.a,method="scharr")
tv=np.array(self.d["tvec"])*10
cd=np.array(self.c["correct_drift"])*10
shift=np.array([25,30])
d1=mag(cd-shift)
d2=mag(tv-(-shift[::-1]))
self.assertLess(d1,1.5,"Drift Correct off by more than 0.1 pxiels.")
self.assertLess(d2,1.5,"Scharr Alignment off by more than 0.1 pxiels.")
a1=ImageFile(self.a1.clone)
a1.as_float()
a1.image=np.sqrt(a1.image)/2+0.25
a1.adjust_contrast()
self.assertEqual(a1.span(),(0.0,1.0),"Either adjust_contrast or span failed with an ImageFile")
# print("#"*80)
# print(self.a.metadata)
# print(self.a1.metadata)
# print(all([k in self.a.metadata.keys() for k in self.a1.metadata.keys()]))
def test_imagefuncs(self):
self.a2.subtract_image(self.a2.image,offset=0)
self.assertTrue(np.all(self.a2.image<=0.0001),"Failed to subtract image from itself")
x=np.linspace(-3*np.pi,3*np.pi,101)
X,Y=np.meshgrid(x,x)
i=ImageFile(np.sin(X)*np.cos(Y))
i2=i.clone
j=i.fft()
self.assertTrue(np.all(np.unique(np.argmax(j,axis=1))==np.array([47,53])),"FFT of image test failed")
j.imshow()
self.assertTrue(len(plt.get_fignums())==1,"Imshow didn't open one window")
plt.close("all")
self.a2.imshow(title=None,figure=None)
self.a2.imshow(title="Hello",figure=1)
self.assertTrue(len(plt.get_fignums())==1,"Imshow with arguments didn't open one window")
plt.close("all")
i=i2
k=i+0.2*X-0.1*Y+0.2
k.level_image(mode="norm")
j=k-i
self.assertLess(np.max(j),0.01,"Level Image failed")
i2=i.clone
i2.quantize([-0.5,0,0.5])
self.assertTrue(np.all(np.unique(i2.data)==np.array([-0.5,0,0.5])),"Quantise levels failed")
i2=i.clone
i2.quantize([-0.5,0,0.5],levels=[-0.25,0.25])
self.assertTrue(np.all(np.unique(i2.data)==np.array([-0.5,0,0.5])),"Quantise levels failed")
i2=i.clone
i2.rotate(np.pi/4)
i2.fft()
self.assertTrue(np.all(np.unique(np.argmax(i2,axis=1))==np.array([46, 47, 49, 50, 51, 53])),"FFT of image test failed")
