def make_ft_axis(length, dt, undersampling = 0, normalized_to_period = 0, zero_in_middle = False, flag_verbose = False):
"""
fourier transform the time axis
20101204/RB: started
20130131/RB: now uses speed of light value from Crocodile.Resources.Constants
INPUT:
length: amount of samples
dt: time between samples
undersampling:
normalized_to_period: will normalize the spectrum to 1 for the specified period. If the number is 0, the spectrum will not be normalized.
zero_in_middle: determines the frequency axes.
OUTPUT:
A frequency axis.
"""
DEBUG.verbose("make FT axis", flag_verbose)
if normalized_to_period == 0:
resolution = 1 / ( CONST.wavenumberToInvFs * length * dt)
else:
resolution = normalized_to_period / (length * dt)
array = numpy.arange((undersampling)*length/2, (undersampling+1)*length/2)*resolution
if zero_in_middle == False:
return numpy.concatenate((array,-numpy.flipud(array)))
else:
return numpy.concatenate((-numpy.flipud(array), array))
def execute(args):
if args.skip1 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(Test_setting_file_stuff)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[0], True)
def make_numpy_ndarray(val):
"""
make a numpy.ndarray out of val, used by make_coordinates()
Types of val that are accepted:
int, float, string: make it a list and then numpy.ndarray.
list: make it a numpy.ndarray
tuple: convert to a list, then numpy.ndarray
numpy.ndarray: return directly
Not accepted:
dict
CHANGELOG:
20130317/RB: started
"""
if type(val) == numpy.ndarray:
return val
elif type(val) == list:
return numpy.array(val)
elif type(val) == dict:
DEBUG.printError("Value shouldn't be a dict or tuple", inspect.stack())
return False
elif type(val) == tuple:
return numpy.array(list(val))
else:
return numpy.array([val])
def execute(args):
if args.skip1 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(Test_find_axes)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[0], True)
if args.skip2 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(Test_make_contours_2d)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[1], True)
if args.skip3 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(Test_find_axes_indices)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[2], True)
if args.skip4 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(Test_truncate_data)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[3], True)
if args.skip5 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(Test_find_subplots)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[4], True)
def truncate_data(data, x_axis, y_axis, x_min_i, x_max_i, y_min_i, y_max_i, flag_verbose = False):
"""
Truncate data in a non-default way.
x_axis = [1,2,3,4,5]
x_min_i = 0
if x_max_i == 2: x_axis = [1,2]
if x_max_i == 4: x_axis = [1,2,3,4]
if x_max_i == -1: x_axis = [1,2,3,4,5]
CHANGELOG:
20130213: was in Plotting.contourplot function, moved to Functions module, now handles x_max_i == -1
"""
DEBUG.verbose("Truncate data", flag_verbose)
if x_max_i == -1:
DEBUG.verbose(" x_max == -1", flag_verbose)
data = data[:,x_min_i:]
x_axis = x_axis[x_min_i:]
else:
DEBUG.verbose(" x_max != -1", flag_verbose)
data = data[:,x_min_i:x_max_i]
x_axis = x_axis[x_min_i:x_max_i]
if y_max_i == -1:
DEBUG.verbose(" y_max == -1", flag_verbose)
data = data[y_min_i:,:]
y_axis = y_axis[y_min_i:]
else:
DEBUG.verbose(" y_max != -1", flag_verbose)
data = data[y_min_i:y_max_i,:]
y_axis = y_axis[y_min_i:y_max_i]
return data, x_axis, y_axis
def test_time_stamp_False(self):
"""
This is correct
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.time_stamp = False
self.assertEqual(self.dc.time_stamp, "False")
def test_time_stamp_5_int(self):
"""
This is correct
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.time_stamp = 12345
self.assertEqual(self.dc.time_stamp, "12345")
def test_import_data_no_data(self):
"""
folder exists, LV_file_format.1 exists and is correct, but contains no other data
"""
self.mess.path = "Test_resources/petw_test_folder_2/"
DEBUG.verbose("\nError about importing is intentional", True)
res = self.mess.import_data(flag_verbose = self.flag_verbose)
self.assertFalse(res)
def test_phase_rad_nan(self):
"""
None sets phase_degrees to init value
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.phase_rad = None
self.assertEqual(self.dc.phase_degrees, None)
self.assertEqual(self.dc.phase_rad, None)
def test_2p_1m(self):
"""
mess[0].s = 1 + [1].s: 2 - [2].s: 3
(1 + 2) / 2 - 3 = -1.5
"""
DEBUG.verbose("\nWarning about zeropad intentional", True)
mer = PEME.pe_merge("Test", class_plus = [self.mess[0], self.mess[1]], class_min = [self.mess[2]], flag_verbose = self.flag_verbose)
self.assertTrue(numpy.all(mer.s == -1.5))
def test_phase_rad_true(self):
"""
True should be interpreted as 1
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.phase_rad = True
self.assertAlmostEqual(self.dc.phase_degrees, 1 * 180 / numpy.pi)
self.assertEqual(self.dc.phase_rad, 1)
def test_phase_rad_nan(self):
"""
numpy.nan should give error, no value is set
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.phase_rad = numpy.nan
self.assertEqual(self.dc.phase_degrees, None)
self.assertEqual(self.dc.phase_rad, None)
def test_phase_rad_false(self):
"""
False should be interpreted as 0
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.phase_rad = False
self.assertEqual(self.dc.phase_degrees, 0)
self.assertEqual(self.dc.phase_rad, 0)
def test_phase_degrees_none(self):
"""
None should will reset phase_degrees to init value
"""
DEBUG.verbose("\nWarning is intentional", True)
self.dc.phase_degrees = None
self.assertEqual(self.dc.phase_degrees, None)
self.assertEqual(self.dc.phase_rad, None)
def test_import_data_incorrect_path(self):
"""
Path is incorrect, no data imported. Returns False
"""
self.mess.path = "Test_resources/FolderDoesNotExist/"
DEBUG.verbose("\nError that directory can't found is intentional", True)
res = self.mess.import_data(flag_verbose = self.flag_verbose)
self.assertFalse(res)
def test_zeropad_to_r_uninit(self):
"""
without r set, it should give an error
"""
DEBUG.verbose("\nError is intentional", True)
self.dc.zeropad_to = 40
self.assertEqual(self.dc.zeropad_to, None)
self.assertEqual(self.dc.zeropad_by, 1.0)
def test_import_data_wrong_file_format(self):
"""
LV_file_format.666 should not be recognized.
"""
self.mess.path = "Test_resources/petw_test_folder_1/"
DEBUG.verbose("\nError about unknown file format is intentional", True)
res = self.mess.import_data(flag_verbose = self.flag_verbose)
self.assertFalse(res)
def test_object_with_sub_type_unknown_sub_type(self):
"""
Test if objects with sub_type 'x' are found - there should be none. This raises a warning. The resulting array has length zero.
"""
sub_type = "x"
DEBUG.verbose("\nWarning is intentional", True)
array = self.oa.list_objects_with_sub_type(sub_type = sub_type, flag_verbose = self.flag_verbose)
self.assertTrue(len(array) == 0)
def test_add_array_with_objects_2(self):
"""
Add unique and a non-unique object to the array
"""
temp = [self.a, self.c]
DEBUG.verbose("\nWarning is intentional", True)
self.oa.add_array_with_objects(temp, flag_verbose = self.flag_verbose)
self.assertTrue(["a", "b", "c"] == self.oa.obj_id_array)
def test_rs_1(self):
"""
This should work correct
r and s exist
"""
DEBUG.verbose("\nTwo intentional zeropad warnings", True)
mer = PEME.pe_merge("Test", class_plus = [self.mess[0]], class_min = [self.mess[1]], flag_verbose = self.flag_verbose)
self.assertTrue(numpy.all(mer.s))
def test_add_object_with_same_obj_id(self):
"""
Add object with same obj_id
"""
a = OA.testobject("Boot", "a", "power", flag_verbose = self.flag_verbose)
DEBUG.verbose("\nError is intentional", True)
result = self.oa.add_object(a, flag_verbose = self.flag_verbose)
self.assertTrue(["a", "b", "c"] == self.oa.obj_id_array and result == False)
def test_add_object_without_obj_id(self):
"""
Add object without obj_id
"""
oa = OA.objectarray("test_new")
DEBUG.verbose("\nError is intentional", True)
result = oa.add_object(1, flag_verbose = self.flag_verbose)
self.assertFalse(result)
def linear(data, x_axis,
x_range = [0, 0],
y_range = [0, 0],
ax = False,
x_label = "",
y_label = "",
title = "",
legend = "",
plot_real = True,
flag_verbose = False):
DEBUG.verbose("linear plot", flag_verbose)
if plot_real:
data = numpy.real(data)
# make the x-axis
if x_range == [0, 0]:
x_min = x_axis[0]
x_max = x_axis[-1]
else:
x_min = x_range[0]
x_max = x_range[1]
# select the appropriate data range
x_min_i = numpy.where(x_axis > x_min)[0][0]
x_max_i = numpy.where(x_axis < x_max)[0][-1]
x_axis = x_axis[x_min_i:x_max_i]
data = data[x_min_i:x_max_i]
# make sure there is an axis-object
if ax == False:
fig = plt.figure()
ax = fig.add_subplot(111)
flag_show = True
else:
flag_show = False
# the actual plot
ax.plot(x_axis, data, label = legend)
ax.set_xlim(x_min, x_max)
if y_range != [0,-1]:
ax.set_ylim(y_range[0], y_range[1])
ax.set_xlabel(x_label)
ax.set_ylabel(y_label)
ax.set_title(title)
if legend != "":
plt.legend()
if flag_show:
plt.show()
return True
def test_obj_id_str(self):
oa = OA.objectarray("test")
a = OA.testobject("Auto", "a", "power", flag_verbose = self.flag_verbose)
oa.add_object(a, flag_verbose = self.flag_verbose)
DEBUG.verbose("\nOverwrite warning is intentional", True)
oa.save_objectarray(self.path_and_filename, flag_overwrite = True, flag_verbose = self.flag_verbose)
def test_reverse_edges(self):
"""
The function does no sanity-checking.
"""
val_min = 27.0
val_max = 22.0
DEBUG.verbose("\nWarning is intentional", True)
res = FU.find_axes_indices(self.axis, val_min, val_max)
self.assertEqual(res, (7,4))
def test_zeropad_to_nan(self):
"""
set zeropad_to to numpy.nan
"""
self.dc.r = [numpy.ones((10,20)), numpy.ones((10,20))]
DEBUG.verbose("\nError is intentional", True)
self.dc.zeropad_to = numpy.nan
self.assertEqual(self.dc.zeropad_to, None)
self.assertEqual(self.dc.zeropad_by, 1.0)
def fourier(array,
zero_in_middle = False,
first_correction = False,
zeropad_to = None,
window_function = "none",
window_length = 0,
flag_plot = False,
flag_verbose = False):
"""
A Fourier transform for any dimension.
INPUT:
- array (x-dimensions ndarray): to be FFT'd
- zero_in_middle (BOOL): for FFT the zero-time should be the first element of the array. If the zero is in the middle, it will be shifted first
- first_correction (BOOL): if the first element of the array has to be halved, check this as True
- zeropad_to (number): Length of the transformed axis of the output. If n is smaller than the length of the input, the input is cropped. If it is larger, the input is padded with zeros. If n is None, the length of the input (along the axis specified by axis) is used.
OUTPUT:
array (x-dimensions ndarray): Fourier transformed array
CHANGELOG:
20101204 RB: started
20110909 RB: added zeropadding
"""
DEBUG.verbose("FFT", flag_verbose)
# shift time = 0 to first element
if zero_in_middle == True:
array = numpy.fft.ifftshift(array)
# half the first element
if first_correction == True:
dim = len(numpy.shape(array))
if dim == 1:
array[0] /= 2
elif dim == 2:
array[0,:] /= 2
array[:,0] /= 2
elif dim > 2:
DEBUG.printError("Correction of the first element is not done!", inspect.stack())
# window function
if window_function != "none":
array = window_functions(array, window_function, window_length, flag_plot = flag_plot)
# the fft
array = numpy.fft.fft(array, n = zeropad_to)
# move the array back if it was shifted
if zero_in_middle == True:
array = numpy.fft.fftshift(array)
return array
def test_phase_degrees_uninit_1(self):
"""
mess[0].phase_degrees = None
s=[0] to suppress zeropad warning
"""
self.mess[0].s = [0]
DEBUG.verbose("\nIntentional phase warning", True)
self.mess[0].phase_degrees = None
DEBUG.verbose("\nIntentional phase warning", True)
mer = PEME.pe_merge("Test", class_plus = [self.mess[0]], class_min = [self.mess[1]], flag_verbose = self.flag_verbose)
self.assertEqual(mer.phase_degrees, None)
def test_obj_id_unicode(self):
"""
This testcase may be unnecesary. If you use from __future__ import unicode_literals, then somes strings are suddenly unicode, giving problems when saving the database. However, in Python 3.3 they removed this. Without the __future__ thingy it also works fine in Python 2.7.
"""
oa = OA.objectarray("test")
l = ["auto"]
a = OA.testobject(l[0], "a", "power", flag_verbose = self.flag_verbose)
oa.add_object(a, flag_verbose = self.flag_verbose)
DEBUG.verbose("\nOverwrite warning is intentional", True)
oa.save_objectarray(self.path_and_filename, flag_overwrite = True, flag_verbose = self.flag_verbose)
def test_phase_degrees_uninit_2(self):
"""
mess[1].phase_degrees = None
s=[0] to suppress zeropad warning
Tests if the order makes a difference. It shouldn't
"""
self.mess[0].s = [0]
DEBUG.verbose("\nIntentional phase warning", True)
self.mess[1].phase_degrees = None
DEBUG.verbose("\nError is intentional", True)
mer = PEME.pe_merge("Test", class_plus = [self.mess[0]], class_min = [self.mess[1]], flag_verbose = self.flag_verbose)
self.assertEqual(mer.phase_degrees, None)
def execute(args):
if args.skip1 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(
Test_make_coordinates)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[0], True)
if args.skip2 == False:
suite = unittest.TestLoader().loadTestsFromTestCase(
Test_find_longest_list)
unittest.TextTestRunner(verbosity=1).run(suite)
else:
DEBUG.verbose("Skipping: " + suite_list[1], True)