def __init__(self,
name='scan0',
arches=[],
data_file='scan0',
scan_data=pd.DataFrame(),
mg_args={'wavelength': 1e-10},
bai_1d_args={},
bai_2d_args={}):
# TODO: add docstring for init
super().__init__()
self.name = name
if arches:
self.arches = pd.Series(arches, index=[a.idx for a in arches])
else:
self.arches = pd.Series()
self.data_file = data_file
self.scan_data = scan_data
self.mg_args = mg_args
self.multi_geo = MultiGeometry([a.integrator for a in arches],
**mg_args)
self.bai_1d_args = bai_1d_args
self.bai_2d_args = bai_2d_args
self.mgi_1d_I = 0
self.mgi_1d_2theta = 0
self.mgi_1d_q = 0
self.mgi_2d_I = 0
self.mgi_2d_2theta = 0
self.mgi_2d_q = 0
self.file_lock = Condition()
self.sphere_lock = Condition()
self.bai_1d = int_1d_data()
self.bai_2d = int_2d_data()
def set_multi_geo(self, **args):
"""Sets the MultiGeometry instance stored in the arch.
args: see pyFAI.multiple_geometry.MultiGeometry
"""
with self.sphere_lock:
self.multi_geo = MultiGeometry([a.integrator for a in self.arches],
**args)
self.mg_args = args
def set_multi_geo(self, **args):
"""Sets the MultiGeometry instance stored in the arch.
args: see pyFAI.multiple_geometry.MultiGeometry. If no args are
passed, uses mg_args attribute. Otherwise, updates
mg_args and uses passed arguments.
"""
self.mg_args.update(args)
with self.sphere_lock:
self.multi_geo = MultiGeometry([a.integrator for a in self.arches],
**self.mg_args)
def add_arch(self,
arch=None,
calculate=True,
update=True,
get_sd=True,
set_mg=True,
**kwargs):
"""Adds new arch to sphere.
args:
arch: EwaldArch instance, arch to be added. Recommended to always
pass a copy of an arch with the arch.copy method
calculate: whether to run the arch's calculate methods after adding
update: bool, if True updates the bai_int attribute
get_sd: bool, if True tries to get scan data from arch
set_mg: bool, if True sets the MultiGeometry attribute. Takes a
long time, especially with longer lists. Recommended to run
set_multi_geo method after all arches are loaded.
returns None
"""
with self.sphere_lock:
if arch is None:
arch = EwaldArch(**kwargs)
if calculate:
arch.integrate_1d(**self.bai_1d_args)
# arch.integrate_2d(**self.bai_2d_args)
arch.file_lock = self.file_lock
self.arches = self.arches.append(pd.Series(arch, index=[arch.idx]))
self.arches.sort_index(inplace=True)
if arch.scan_info and get_sd:
ser = pd.Series(arch.scan_info, dtype='float64')
if list(self.scan_data.columns):
try:
self.scan_data.loc[arch.idx] = ser
except ValueError:
print('Mismatched columns')
else:
self.scan_data = pd.DataFrame(arch.scan_info,
index=[arch.idx],
dtype='float64')
self.scan_data.sort_index(inplace=True)
if update:
self._update_bai_1d(arch)
# self._update_bai_2d(arch)
if set_mg:
self.multi_geo = MultiGeometry(
[a.integrator for a in self.arches], **self.mg_args)
def __init__(self):
self.headermodel = None
self.selectionmodel = None
self.multiAI = MultiGeometry([])
self.AIs = dict()
widget = ParameterTree()
energy = SimpleParameter(name='Energy',
type='float',
value=10000,
siPrefix=True,
suffix='eV')
wavelength = SimpleParameter(name='Wavelength',
type='float',
value=1.239842e-6 / 10000,
siPrefix=True,
suffix='m')
self.parameter = Parameter(name="Device Profiles",
type='group',
children=[energy, wavelength])
widget.setParameters(self.parameter, showTop=False)
icon = QIcon(str(path('icons/calibrate.png')))
super(DeviceProfiles, self).__init__(icon, "Device Profiles", widget)
self.parameter.sigValueChanged.connect(self.sigRequestRedraw)
self.parameter.sigValueChanged.connect(self.sigRequestReduce)
self.parameter.sigTreeStateChanged.connect(self.simulateCalibrant)
self.parameter.sigTreeStateChanged.connect(self.genAIs)
self.parameter.sigValueChanged.connect(self.simulateCalibrant)
def __init__(self):
self.headermodel = None
self.selectionmodel = None
self.multiAI = MultiGeometry([])
self.AIs = dict()
self._changes = []
self.isSilent = False
energy = SimpleParameter(name='Energy',
type='float',
value=10000,
siPrefix=True,
suffix='eV')
wavelength = SimpleParameter(name='Wavelength',
type='float',
value=1.239842e-6 / 10000,
siPrefix=True,
suffix='m')
icon = QIcon(str(path('icons/calibrate.png')))
super(DeviceProfiles, self).__init__(icon,
"Device Profiles",
[energy, wavelength],
addText='New Device')
self.sigTreeStateChanged.connect(self.stateChanged)
def cake_saxs(inpaints,
ais,
masks,
radial_range=(0, 60),
azimuth_range=(-90, 90),
npt_rad=250,
npt_azim=250):
"""
Unwrapp the stitched image from q-space to 2theta-Chi space (Radial-Azimuthal angle)
Parameters:
-----------
:param inpaints: List of 2D inpainted images
:type inpaints: List of ndarray
:param ais: List of AzimuthalIntegrator/Transform generated using pyGIX/pyFAI which contain the information about the experiment geometry
:type ais: list of AzimuthalIntegrator / TransformIntegrator
:param masks: List of 2D image (same dimension as inpaints)
:type masks: List of ndarray
:param radial_range: minimum and maximum of the radial range in degree
:type radial_range: Tuple
:param azimuth_range: minimum and maximum of the 2th range in degree
:type azimuth_range: Tuple
:param npt_rad: number of point in the radial range
:type npt_rad: int
:param npt_azim: number of point in the azimuthal range
:type npt_azim: int
"""
mg = MultiGeometry(ais,
unit='q_A^-1',
radial_range=radial_range,
azimuth_range=azimuth_range,
wavelength=None,
empty=0.0,
chi_disc=180)
cake, q, chi = mg.integrate2d(lst_data=inpaints,
npt_rad=npt_rad,
npt_azim=npt_azim,
correctSolidAngle=True,
lst_mask=masks)
return cake, q, chi[::-1]
def integrate_rad_saxs(inpaints,
ais,
masks,
radial_range=(0, 40),
azimuth_range=(0, 90),
npt=2000):
"""
Radial integration of transmission data using the pyFAI multigeometry module
Parameters:
-----------
:param inpaints: List of 2D inpainted images
:type inpaints: List of ndarray
:param ais: List of AzimuthalIntegrator/Transform generated using pyGIX/pyFAI which contain the information about the experiment geometry
:type ais: list of AzimuthalIntegrator / TransformIntegrator
:param masks: List of 2D image (same dimension as inpaints)
:type masks: List of ndarray
:param radial_range: minimum and maximum of the radial range in degree
:type radial_range: Tuple
:param azimuth_range: minimum and maximum of the 2th range in degree
:type azimuth_range: Tuple
:param npt: number of point of the final 1D profile
:type npt: int
"""
mg = MultiGeometry(ais,
unit='q_A^-1',
radial_range=radial_range,
azimuth_range=azimuth_range,
wavelength=None,
empty=-1,
chi_disc=180)
q, i_rad = mg.integrate1d(lst_data=inpaints,
npt=npt,
correctSolidAngle=True,
lst_mask=masks)
return q, i_rad
def createMg (aifiles = None):
if (aifiles == None):
root = Tk()
aifiles = filedialog.askopenfilenames(parent=root, title='Choose multiple files')
aifiles = root.tk.splitlist(aifiles)
print (aifiles)
root.destroy()
ais = []
for file in aifiles:
ais.append(pyFAI.load(file))
mg = MultiGeometry(ais, unit = "2th_deg", radial_range= (25,75) )
print (mg)
return (mg)
def setUp(self):
unittest.TestCase.setUp(self)
self.data = fabio.open(UtilsTest.getimage("1788/moke.tif")).data
self.lst_data = [
self.data[:250, :300], self.data[250:, :300],
self.data[:250, 300:], self.data[250:, 300:]
]
self.det = Detector(1e-4, 1e-4)
self.det.max_shape = (500, 600)
self.sub_det = Detector(1e-4, 1e-4)
self.sub_det.max_shape = (250, 300)
self.ai = AzimuthalIntegrator(0.1, 0.03, 0.03, detector=self.det)
self.range = (0, 23)
self.ais = [
AzimuthalIntegrator(0.1, 0.030, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.030, 0.00, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.00, detector=self.sub_det),
]
self.mg = MultiGeometry(self.ais,
radial_range=self.range,
unit="2th_deg")
self.N = 390
def setUp(self):
unittest.TestCase.setUp(self)
self.data = fabio.open(UtilsTest.getimage("1788/moke.tif")).data
self.lst_data = [self.data[:250, :300], self.data[250:, :300], self.data[:250, 300:], self.data[250:, 300:]]
self.det = Detector(1e-4, 1e-4)
self.det.max_shape = (500, 600)
self.sub_det = Detector(1e-4, 1e-4)
self.sub_det.max_shape = (250, 300)
self.ai = AzimuthalIntegrator(0.1, 0.03, 0.03, detector=self.det)
self.range = (0, 23)
self.ais = [AzimuthalIntegrator(0.1, 0.030, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.030, 0.00, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.00, detector=self.sub_det),
]
self.mg = MultiGeometry(self.ais, radial_range=self.range, unit="2th_deg")
self.N = 390
def __init__(self):
self.headermodel = None
self.selectionmodel = None
self.multiAI = MultiGeometry([])
self.AIs = dict()
energy = SimpleParameter(name='Energy',
type='float',
value=10000,
siPrefix=True,
suffix='eV')
wavelength = SimpleParameter(name='Wavelength',
type='float',
value=1.239842e-6 / 10000,
siPrefix=True,
suffix='m')
incidentAngle = SimpleParameter(name='Incident Angle',
type='float',
value=90,
siPrefix=False,
suffix=u'°',
limits=(0, 90))
reflection = SimpleParameter(name='Reflection',
type='int',
value=0,
siPrefix=False,
limits=(0, 1),
step=1)
icon = QIcon(str(path('icons/calibrate.png')))
super(DeviceProfiles,
self).__init__(icon,
"Device Profiles",
[energy, wavelength, incidentAngle, reflection],
addText='New Device')
self.sigTreeStateChanged.connect(self.simulateCalibrant)
self.sigTreeStateChanged.connect(self.genAIs)
self.sigTreeStateChanged.connect(self.geometryChanged)
self.sigGeometryChanged.connect(self.save)
class TestMultiGeometry(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.data = fabio.open(UtilsTest.getimage("1788/moke.tif")).data
self.lst_data = [self.data[:250, :300], self.data[250:, :300], self.data[:250, 300:], self.data[250:, 300:]]
self.det = Detector(1e-4, 1e-4)
self.det.max_shape = (500, 600)
self.sub_det = Detector(1e-4, 1e-4)
self.sub_det.max_shape = (250, 300)
self.ai = AzimuthalIntegrator(0.1, 0.03, 0.03, detector=self.det)
self.range = (0, 23)
self.ais = [AzimuthalIntegrator(0.1, 0.030, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.030, 0.00, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.00, detector=self.sub_det),
]
self.mg = MultiGeometry(self.ais, radial_range=self.range, unit="2th_deg")
self.N = 390
def tearDown(self):
unittest.TestCase.tearDown(self)
self.data = None
self.lst_data = None
self.det = None
self.sub_det = None
self.ai = None
self.ais = None
self.mg = None
def test_integrate1d(self):
tth_ref, I_ref = self.ai.integrate1d(self.data, radial_range=self.range, npt=self.N, unit="2th_deg", method="splitpixel")
obt = self.mg.integrate1d(self.lst_data, self.N)
tth_obt, I_obt = obt
self.assertEqual(abs(tth_ref - tth_obt).max(), 0, "Bin position is the same")
# intensity need to be scaled by solid angle 1e-4*1e-4/0.1**2 = 1e-6
delta = (abs(I_obt * 1e6 - I_ref).max())
self.assertLessEqual(delta, 5e-5, "Intensity is the same delta=%s" % delta)
def test_integrate2d(self):
ref = self.ai.integrate2d(self.data, self.N, 360, radial_range=self.range, azimuth_range=(-180, 180), unit="2th_deg", method="splitpixel", all=True)
obt = self.mg.integrate2d(self.lst_data, self.N, 360, all=True)
self.assertEqual(abs(ref["radial"] - obt["radial"]).max(), 0, "Bin position is the same")
self.assertEqual(abs(ref["azimuthal"] - obt["azimuthal"]).max(), 0, "Bin position is the same")
# intensity need to be scaled by solid angle 1e-4*1e-4/0.1**2 = 1e-6
delta = abs(obt["I"] * 1e6 - ref["I"])[obt["count"] >= 1] # restict on valid pixel
delta_cnt = abs(obt["count"] - ref["count"])
delta_sum = abs(obt["sum"] * 1e6 - ref["sum"])
if delta.max() > 1:
logger.warning("TestMultiGeometry.test_integrate2d gave intensity difference of %s" % delta.max())
if logger.level <= logging.DEBUG:
from matplotlib import pyplot as plt
f = plt.figure()
a1 = f.add_subplot(2, 2, 1)
a1.imshow(ref["sum"])
a2 = f.add_subplot(2, 2, 2)
a2.imshow(obt["sum"])
a3 = f.add_subplot(2, 2, 3)
a3.imshow(delta_sum)
a4 = f.add_subplot(2, 2, 4)
a4.plot(delta_sum.sum(axis=0))
f.show()
raw_input()
self.assertLess(delta_cnt.max(), 0.001, "pixel count is the same delta=%s" % delta_cnt.max())
self.assertLess(delta_sum.max(), 0.03, "pixel sum is the same delta=%s" % delta_sum.max())
self.assertLess(delta.max(), 0.004, "pixel intensity is the same (for populated pixels) delta=%s" % delta.max())
def run_integration(configFile, peak_detection_ratio=0.1):
Run = RunInit(configFile)
params = Run.params
mask = fabio.open(params.maskFile).data
number_of_run = Run.number_of_run
image_extension = params.image_extension
img_folder = params.img_folder
img_prefix = params.img_prefix
img_digit = int(params.img_digit)
poni_files = params.poni_files
img_begin = np.asarray(params.img_begin)
img_end = np.asarray(params.img_end)
Qlength = [
np.sqrt((Run.all_Q0[r]**2).sum(axis=2)) for r in range(number_of_run)
]
m = np.array([q.min() for q in Qlength])
M = np.array([q.max() for q in Qlength])
Qmin = m.min()
Qmax = M.max()
print("Q min = %f" % Qmin)
print("Q max = %f" % Qmax)
maxipix = pyFAI.detector_factory("Maxipix_5x1")
ais = [pyFAI.load(pf) for pf in poni_files]
for ai in ais:
ai.detector = maxipix
wl = ai.wavelength * 1e10
tth_min = np.degrees(np.arcsin(Qmin * wl / 4 / np.pi)) * 2
tth_max = np.degrees(np.arcsin(Qmax * wl / 4 / np.pi)) * 2
print("tth min = %f" % tth_min)
print("tth max = %f" % tth_max)
allData = Run.allData_allRun
mg = MultiGeometry(poni_files, radial_range=(tth_min, tth_max))
phi_points = allData.shape[1]
bin_pts = 1000
I_tot = np.zeros(bin_pts)
num_threads = _NUM_THREADS
# """
for j in range(0, phi_points, num_threads):
threads = []
for i in range(j, j + num_threads):
if i < phi_points:
img_data = allData[:, i, :, :]
thr = Integrator(mg, i, img_data, mask, bin_pts)
thr.start()
threads.append(thr)
for thr in threads:
thr.join()
I_tot += thr.I
# """
I_tot = I_tot / phi_points
q_tth = np.linspace(Qmin, Qmax, bin_pts)
tth_q = np.linspace(tth_min, tth_max, bin_pts)
outData = np.vstack([tth_q, q_tth, I_tot])
outData = outData.T
outFile = splitext(configFile)[0] + "_Integrated_intensity_Q.dat"
np.savetxt(outFile,
outData,
header=str("2Theta (deg) \t Q (1/A) \t Intensity"),
fmt="%6.4f")
(tth_peak, I_peak) = get_maxima(thr.tth,
I_tot,
threshold=peak_detection_ratio)
tth_peak = np.asarray(tth_peak)
Q_shell = 4 * np.pi * np.sin(np.radians(tth_peak / 2)) / wl
Qout = np.vstack([tth_peak, Q_shell])
Qout = Qout.T
outFile2 = splitext(configFile)[0] + "_tth_Q_peaks.dat"
np.savetxt(outFile2,
Qout,
fmt="%6.4f",
header=str("Q max = %.4f\n2Theta (deg) \t Q value (1/A)" %
Qmax))
print("TTH peaks: ")
print(tth_peak)
fig = figure()
ax = fig.add_subplot(111)
ax.plot(thr.tth, I_tot, lw=2)
ax.plot(tth_peak, I_peak, "ro")
# for x in tth_peak:
# ax.axvline(x, color="r", lw=1)
ax.set_xlabel("2Theta (deg)")
ax.set_ylabel("Summed intensity (a.u.)")
title = splitext(configFile)[0] + " integrated intensity over phi scan"
ax.set_title(title)
show()
saveImg = splitext(configFile)[0] + "_integrated_intensity.png"
fig.savefig(saveImg)
def __init__(self,
name='scan0',
arches=[],
data_file=None,
scan_data=pd.DataFrame(),
mg_args={'wavelength': 1e-10},
bai_1d_args={},
bai_2d_args={},
static=False,
gi=False,
th_mtr='th',
overall_raw=0,
single_img=False,
global_mask=None,
poni_dict={}):
"""name: string, name of sphere object.
arches: list of EwaldArch object, data to intialize with
data_file: str, path to hdf5 file where data is stored
scan_data: DataFrame, scan metadata
mg_args: dict, arguments for Multigeometry. Must include at
least 'wavelength' attribute in Angstroems
bai_1d_args: dict, arguments for the integrate1d method of pyFAI
AzimuthalIntegrator
bai_2d_args: dict, arguments for the integrate2d method of pyFAI
AzimuthalIntegrator
"""
super().__init__()
self.file_lock = Condition()
if name is None:
self.name = os.path.split(data_file)[-1].split('.')[0]
else:
self.name = name
if data_file is None:
self.data_file = name + ".hdf5"
else:
self.data_file = data_file
self.static = static
self.gi = gi
self.th_mtr = th_mtr
self.single_img = single_img
if arches:
self.arches = ArchSeries(self.data_file,
self.file_lock,
arches,
static=self.static,
gi=self.gi)
else:
self.arches = ArchSeries(self.data_file,
self.file_lock,
static=self.static,
gi=self.gi)
self.scan_data = scan_data
self.mg_args = mg_args
self.multi_geo = MultiGeometry([a.integrator for a in arches],
**mg_args)
self.bai_1d_args = bai_1d_args
self.bai_2d_args = bai_2d_args
self.mgi_1d = int_1d_data()
self.mgi_2d = int_2d_data()
self.sphere_lock = Condition(_PyRLock())
if self.static:
self.bai_1d = int_1d_data_static()
self.bai_2d = int_2d_data_static()
else:
self.bai_1d = int_1d_data()
self.bai_2d = int_2d_data()
self.overall_raw = overall_raw
self.global_mask = global_mask
self.poni_dict = poni_dict
class TestMultiGeometry(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.data = fabio.open(UtilsTest.getimage("1788/moke.tif")).data
self.lst_data = [
self.data[:250, :300], self.data[250:, :300],
self.data[:250, 300:], self.data[250:, 300:]
]
self.det = Detector(1e-4, 1e-4)
self.det.max_shape = (500, 600)
self.sub_det = Detector(1e-4, 1e-4)
self.sub_det.max_shape = (250, 300)
self.ai = AzimuthalIntegrator(0.1, 0.03, 0.03, detector=self.det)
self.range = (0, 23)
self.ais = [
AzimuthalIntegrator(0.1, 0.030, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.03, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.030, 0.00, detector=self.sub_det),
AzimuthalIntegrator(0.1, 0.005, 0.00, detector=self.sub_det),
]
self.mg = MultiGeometry(self.ais,
radial_range=self.range,
unit="2th_deg")
self.N = 390
def tearDown(self):
unittest.TestCase.tearDown(self)
self.data = None
self.lst_data = None
self.det = None
self.sub_det = None
self.ai = None
self.ais = None
self.mg = None
def test_integrate1d(self):
tth_ref, I_ref = self.ai.integrate1d(self.data,
radial_range=self.range,
npt=self.N,
unit="2th_deg",
method="splitpixel")
obt = self.mg.integrate1d(self.lst_data, self.N)
tth_obt, I_obt = obt
self.assertEqual(
abs(tth_ref - tth_obt).max(), 0, "Bin position is the same")
# intensity need to be scaled by solid angle 1e-4*1e-4/0.1**2 = 1e-6
delta = (abs(I_obt * 1e6 - I_ref).max())
self.assert_(delta < 5e-5, "Intensity is the same delta=%s" % delta)
def test_integrate2d(self):
ref = self.ai.integrate2d(self.data,
self.N,
360,
radial_range=self.range,
azimuth_range=(-180, 180),
unit="2th_deg",
method="splitpixel",
all=True)
obt = self.mg.integrate2d(self.lst_data, self.N, 360, all=True)
self.assertEqual(
abs(ref["radial"] - obt["radial"]).max(), 0,
"Bin position is the same")
self.assertEqual(
abs(ref["azimuthal"] - obt["azimuthal"]).max(), 0,
"Bin position is the same")
# intensity need to be scaled by solid angle 1e-4*1e-4/0.1**2 = 1e-6
delta = abs(obt["I"] * 1e6 -
ref["I"])[obt["count"] >= 1e-6] # restrict on valid pixel
delta_cnt = abs(obt["count"] - ref["count"])
delta_sum = abs(obt["sum"] * 1e6 - ref["sum"])
if delta.max() > 0:
logger.warning(
"TestMultiGeometry.test_integrate2d gave intensity difference of %s"
% delta.max())
if logger.level <= logging.DEBUG:
from matplotlib import pyplot as plt
f = plt.figure()
a1 = f.add_subplot(2, 2, 1)
a1.imshow(ref["sum"])
a2 = f.add_subplot(2, 2, 2)
a2.imshow(obt["sum"])
a3 = f.add_subplot(2, 2, 3)
a3.imshow(delta_sum)
a4 = f.add_subplot(2, 2, 4)
a4.plot(delta_sum.sum(axis=0))
f.show()
raw_input()
self.assert_(delta_cnt.max() < 0.001,
"pixel count is the same delta=%s" % delta_cnt.max())
self.assert_(delta_sum.max() < 0.03,
"pixel sum is the same delta=%s" % delta_sum.max())
self.assert_(
delta.max() < 0.004,
"pixel intensity is the same (for populated pixels) delta=%s" %
delta.max())
def add_arch(self,
arch=None,
calculate=True,
update=True,
get_sd=True,
set_mg=True,
**kwargs):
"""Adds new arch to sphere.
args:
arch: EwaldArch instance, arch to be added. Recommended to
always pass a copy of an arch with the arch.copy method
or intialize with kwargs
calculate: whether to run the arch's calculate methods after
adding
update: bool, if True updates the bai_1d and bai_2d
attributes
get_sd: bool, if True tries to get scan data from arch
set_mg: bool, if True sets the MultiGeometry attribute.
Takes a long time, especially with longer lists.
Recommended to run set_multi_geo method after all arches
are loaded.
kwargs: If arch is None, used to intialize the EwaldArch,
see EwaldArch for arguments.
returns None
"""
with self.sphere_lock:
if arch is None:
arch = EwaldArch(**kwargs)
if calculate:
arch.integrate_1d(global_mask=self.global_mask,
**self.bai_1d_args)
arch.integrate_2d(global_mask=self.global_mask,
**self.bai_2d_args)
arch.file_lock = self.file_lock
self.arches = self.arches.append(pd.Series(arch, index=[arch.idx]))
self.arches.sort_index(inplace=True)
if arch.scan_info and get_sd:
ser = pd.Series(arch.scan_info, dtype='float64')
if list(self.scan_data.columns):
try:
self.scan_data.loc[arch.idx] = ser
except ValueError:
print('Mismatched columns')
else:
self.scan_data = pd.DataFrame(arch.scan_info,
index=[arch.idx],
dtype='float64')
self.scan_data.sort_index(inplace=True)
with self.file_lock:
with utils.catch_h5py_file(self.data_file, 'a') as file:
compression = 'lzf'
if self.static:
compression = None
utils.dataframe_to_h5(self.scan_data, file,
'scan_data', compression)
if update:
self._update_bai_1d(arch)
self._update_bai_2d(arch)
if set_mg:
self.multi_geo = MultiGeometry(
[a.integrator for a in self.arches], **self.mg_args)
self.overall_raw += arch.map_raw
class EwaldSphere:
"""Class for storing multiple arch objects, and stores a MultiGeometry
integrator from pyFAI.
Attributes:
arches: ArchSeries, list of arches indexed by their idx value
bai_1d: int_1d_data object, stores result of 1d integration
bai_1d_args: dict, arguments for invidivual arch integrate1d
method
bai_2d: int_2d_data object, stores result of 2d integration
bai_2d_args: dict, arguments for invidivual arch integrate2d
method
data_file: str, file to save data to
file_lock: lock for ensuring one writer to hdf5 file
mg_args: arguments for MultiGeometry constructor
mgi_1d: int_1d_data object, stores result from multigeometry
integrate1d method
mgi_2d: int_2d_data object, stores result from multigeometry
integrate2d method
multi_geo: MultiGeometry instance
name: str, name of the sphere
scan_data: DataFrame, stores all scan metadata
sphere_lock: lock for modifying data in sphere
Methods:
add_arch: adds new arch and optionally updates other data
by_arch_integrate_1d: Runs 1 dimensional integration of each
arch individually and sums the result, stored in bai_1d
by_arch_integrate_2d: Runs 2 dimensional integration of each
arch individually and sums the result, stored in bai_2d
load_from_h5: loads data from hdf5 file
set_multi_geo: sets the MultiGeometry instance
multigeometry_integrate_1d: wrapper for MultiGeometry
integrate1d method, result stored in mgi_1d
multigeometry_integrate_2d: wrapper for MultiGeometry
integrate2d method, result stored in mgi_2d
save_bai_1d: Saves only bai_1d to the data_file
save_bai_2d: Saves only bai_2d to the data_file
save_to_h5: saves data to hdf5 file
set_multi_geo: instatiates the multigeometry object, or
overrides it if it already exists.
"""
def __init__(self,
name='scan0',
arches=[],
data_file=None,
scan_data=pd.DataFrame(),
mg_args={'wavelength': 1e-10},
bai_1d_args={},
bai_2d_args={},
static=False,
gi=False,
th_mtr='th',
overall_raw=0,
single_img=False,
global_mask=None,
poni_dict={}):
"""name: string, name of sphere object.
arches: list of EwaldArch object, data to intialize with
data_file: str, path to hdf5 file where data is stored
scan_data: DataFrame, scan metadata
mg_args: dict, arguments for Multigeometry. Must include at
least 'wavelength' attribute in Angstroems
bai_1d_args: dict, arguments for the integrate1d method of pyFAI
AzimuthalIntegrator
bai_2d_args: dict, arguments for the integrate2d method of pyFAI
AzimuthalIntegrator
"""
super().__init__()
self.file_lock = Condition()
if name is None:
self.name = os.path.split(data_file)[-1].split('.')[0]
else:
self.name = name
if data_file is None:
self.data_file = name + ".hdf5"
else:
self.data_file = data_file
self.static = static
self.gi = gi
self.th_mtr = th_mtr
self.single_img = single_img
if arches:
self.arches = ArchSeries(self.data_file,
self.file_lock,
arches,
static=self.static,
gi=self.gi)
else:
self.arches = ArchSeries(self.data_file,
self.file_lock,
static=self.static,
gi=self.gi)
self.scan_data = scan_data
self.mg_args = mg_args
self.multi_geo = MultiGeometry([a.integrator for a in arches],
**mg_args)
self.bai_1d_args = bai_1d_args
self.bai_2d_args = bai_2d_args
self.mgi_1d = int_1d_data()
self.mgi_2d = int_2d_data()
self.sphere_lock = Condition(_PyRLock())
if self.static:
self.bai_1d = int_1d_data_static()
self.bai_2d = int_2d_data_static()
else:
self.bai_1d = int_1d_data()
self.bai_2d = int_2d_data()
self.overall_raw = overall_raw
self.global_mask = global_mask
self.poni_dict = poni_dict
def reset(self):
"""Resets all held data objects to blank state, called when all
new data is going to be loaded or when a sphere needs to be
purged of old data.
"""
with self.sphere_lock:
self.scan_data = pd.DataFrame()
self.mgi_1d = int_1d_data()
self.mgi_2d = int_2d_data()
self.arches = ArchSeries(self.data_file,
self.file_lock,
static=self.static,
gi=self.gi)
self.global_mask = None
if self.static:
self.bai_1d = int_1d_data_static()
self.bai_2d = int_2d_data_static()
else:
self.bai_1d = int_1d_data()
self.bai_2d = int_2d_data()
self.overall_raw = 0
def add_arch(self,
arch=None,
calculate=True,
update=True,
get_sd=True,
set_mg=True,
**kwargs):
"""Adds new arch to sphere.
args:
arch: EwaldArch instance, arch to be added. Recommended to
always pass a copy of an arch with the arch.copy method
or intialize with kwargs
calculate: whether to run the arch's calculate methods after
adding
update: bool, if True updates the bai_1d and bai_2d
attributes
get_sd: bool, if True tries to get scan data from arch
set_mg: bool, if True sets the MultiGeometry attribute.
Takes a long time, especially with longer lists.
Recommended to run set_multi_geo method after all arches
are loaded.
kwargs: If arch is None, used to intialize the EwaldArch,
see EwaldArch for arguments.
returns None
"""
with self.sphere_lock:
if arch is None:
arch = EwaldArch(**kwargs)
if calculate:
arch.integrate_1d(global_mask=self.global_mask,
**self.bai_1d_args)
arch.integrate_2d(global_mask=self.global_mask,
**self.bai_2d_args)
arch.file_lock = self.file_lock
self.arches = self.arches.append(pd.Series(arch, index=[arch.idx]))
self.arches.sort_index(inplace=True)
if arch.scan_info and get_sd:
ser = pd.Series(arch.scan_info, dtype='float64')
if list(self.scan_data.columns):
try:
self.scan_data.loc[arch.idx] = ser
except ValueError:
print('Mismatched columns')
else:
self.scan_data = pd.DataFrame(arch.scan_info,
index=[arch.idx],
dtype='float64')
self.scan_data.sort_index(inplace=True)
with self.file_lock:
with utils.catch_h5py_file(self.data_file, 'a') as file:
compression = 'lzf'
if self.static:
compression = None
utils.dataframe_to_h5(self.scan_data, file,
'scan_data', compression)
if update:
self._update_bai_1d(arch)
self._update_bai_2d(arch)
if set_mg:
self.multi_geo = MultiGeometry(
[a.integrator for a in self.arches], **self.mg_args)
self.overall_raw += arch.map_raw
def by_arch_integrate_1d(self, **args):
"""Integrates all arches individually, then sums the results for
the overall integration result.
args: see EwaldArch.integrate_1d. If any args are passed, the
bai_1d_args dictionary is also updated with the new args.
If no args are passed, uses bai_1d_args attribute.
"""
if not args:
args = self.bai_1d_args
else:
self.bai_1d_args = args.copy()
with self.sphere_lock:
if self.static:
self.bai_1d = int_1d_data_static()
else:
self.bai_1d = int_1d_data()
for arch in self.arches:
arch.integrate_1d(global_mask=self.global_mask, **args)
self.arches[arch.idx] = arch
self._update_bai_1d(arch)
def by_arch_integrate_2d(self, **args):
"""Integrates all arches individually, then sums the results for
the overall integration result.
args: see EwaldArch.integrate_2d. If any args are passed, the
bai_2d_args dictionary is also updated with the new args.
If no args are passed, uses bai_2d_args attribute.
"""
if not args:
args = self.bai_2d_args
else:
self.bai_2d_args = args.copy()
with self.sphere_lock:
if self.static:
self.bai_2d = int_2d_data_static()
else:
self.bai_2d = int_2d_data()
for arch in self.arches:
arch.integrate_2d(global_mask=self.global_mask, **args)
self.arches[arch.idx] = arch
self._update_bai_2d(arch)
def _update_bai_1d(self, arch):
"""helper function to update overall bai variables.
"""
with self.sphere_lock:
try:
assert list(self.bai_1d.raw.shape) == list(
arch.int_1d.raw.shape)
except (AssertionError, AttributeError):
if not self.static:
self.bai_1d.raw = np.zeros(arch.int_1d.raw.shape)
self.bai_1d.pcount = np.zeros(arch.int_1d.pcount.shape)
self.bai_1d.norm = np.zeros(arch.int_1d.norm.shape)
self.bai_1d.sigma = np.zeros(arch.int_1d.norm.shape)
self.bai_1d.sigma_raw = np.zeros(arch.int_1d.norm.shape)
try:
self.bai_1d += arch.int_1d
self.bai_1d.ttheta = arch.int_1d.ttheta
self.bai_1d.q = arch.int_1d.q
except AttributeError:
pass
self.save_bai_1d()
def _update_bai_2d(self, arch):
"""helper function to update overall bai variables.
"""
with self.sphere_lock:
try:
# assert self.bai_2d.raw.shape == arch.int_2d.raw.shape
if self.static:
assert self.bai_2d.i_qChi.shape == arch.int_2d.i_qChi.shape
else:
assert self.bai_2d.norm.shape == arch.int_2d.norm.shape
except (AssertionError, AttributeError):
if self.static:
self.bai_2d.i_qChi = np.zeros(arch.int_2d.i_qChi.shape)
self.bai_2d.i_tthChi = np.zeros(arch.int_2d.i_tthChi.shape)
self.bai_2d.i_QxyQz = np.zeros(arch.int_2d.i_QxyQz.shape)
else:
self.bai_2d.norm = np.zeros(arch.int_2d.norm.shape)
self.bai_2d.raw = np.zeros(arch.int_2d.raw.shape)
self.bai_2d.pcount = np.zeros(arch.int_2d.pcount.shape)
self.bai_2d.sigma = np.zeros(arch.int_2d.norm.shape)
self.bai_2d.sigma_raw = np.zeros(arch.int_2d.norm.shape)
try:
self.bai_2d.ttheta = arch.int_2d.ttheta
self.bai_2d.q = arch.int_2d.q
self.bai_2d.chi = arch.int_2d.chi
if not self.static:
self.bai_2d += arch.int_2d
else:
self.bai_2d.i_qChi += arch.int_2d.i_qChi
self.bai_2d.i_tthChi += arch.int_2d.i_tthChi
self.bai_2d.i_QxyQz += arch.int_2d.i_QxyQz
self.bai_2d.qz = arch.int_2d.qz
self.bai_2d.qxy = arch.int_2d.qxy
except AttributeError:
pass
self.save_bai_2d()
def set_multi_geo(self, **args):
"""Sets the MultiGeometry instance stored in the arch.
args: see pyFAI.multiple_geometry.MultiGeometry. If no args are
passed, uses mg_args attribute. Otherwise, updates
mg_args and uses passed arguments.
"""
self.mg_args.update(args)
with self.sphere_lock:
self.multi_geo = MultiGeometry([a.integrator for a in self.arches],
**self.mg_args)
def multigeometry_integrate_1d(self, monitor=None, **kwargs):
"""Wrapper for integrate1d method of MultiGeometry.
args:
monitor: channel with normalization value
kwargs: see MultiGeometry.integrate1d
returns:
result: result from MultiGeometry.integrate1d
"""
with self.sphere_lock:
lst_mask = [a.get_mask() for a in self.arches]
if monitor is None:
try:
result = self.multi_geo.integrate1d(
[a.map_norm for a in self.arches],
lst_mask=lst_mask,
**kwargs)
except Exception as e:
print(e)
print('Exception 1')
result = self.multi_geo.integrate1d(
[a.map_raw for a in self.arches],
lst_mask=lst_mask,
**kwargs)
else:
result = self.multi_geo.integrate1d(
[a.map_raw for a in self.arches],
lst_mask=lst_mask,
normalization_factor=list(self.scan_data[monitor]),
**kwargs)
self.mgi_1d.from_result(result, self.multi_geo.wavelength)
return result
def multigeometry_integrate_2d(self, monitor=None, **kwargs):
"""Wrapper for integrate1d method of MultiGeometry.
args:
monitor: channel with normalization value
kwargs: see MultiGeometry.integrate1d
returns:
result: result from MultiGeometry.integrate1d
"""
with self.sphere_lock:
lst_mask = [a.get_mask() for a in self.arches]
if monitor is None:
try:
result = self.multi_geo.integrate2d(
[a.map_raw / a.map_norm for a in self.arches],
lst_mask=lst_mask,
**kwargs)
except Exception as e:
print(e)
print('Exception 2')
result = self.multi_geo.integrate2d(
[a.map_raw for a in self.arches],
lst_mask=lst_mask,
**kwargs)
else:
result = self.multi_geo.integrate2d(
[a.map_raw for a in self.arches],
lst_mask=lst_mask,
normalization_factor=list(self.scan_data[monitor]),
**kwargs)
self.mgi_2d.from_result(result, self.multi_geo.wavelength)
return result
def save_to_h5(self, replace=False, *args, **kwargs):
"""Saves data to hdf5 file.
args:
replace: bool, if True file is truncated prior to writing
data.
arches: list, list of arch ids to save. Deprecated.
data_onle: bool, if true only saves the scan_data attribute
and does not save mg_args, bai_1d_args, or bai_2d_args.
compression: str, what compression algorithm to pass to
h5py. See h5py documentation for acceptable compression
algorithms.
"""
if replace:
mode = 'w'
else:
mode = 'a'
with self.file_lock:
with utils.catch_h5py_file(self.data_file, mode) as file:
self._save_to_h5(file, *args, **kwargs)
def _save_to_h5(self,
grp,
arches=None,
data_only=False,
compression='lzf'):
"""Actual function for saving data, run with the file open and
holding the file_lock.
"""
if self.static:
compression = None
with self.sphere_lock:
grp.attrs['type'] = 'EwaldSphere'
if data_only:
lst_attr = [
"scan_data",
"global_mask",
"overall_raw",
]
else:
lst_attr = [
"scan_data", "global_mask", "mg_args", "bai_1d_args",
"bai_2d_args", "overall_raw", "static", "gi", "th_mtr",
"single_img", "poni_dict"
]
utils.attributes_to_h5(self,
grp,
lst_attr,
compression=compression)
keys = ('bai_1d', 'bai_2d', 'mgi_1d', 'mgi_2d')
if self.static:
keys = ('bai_1d', 'bai_2d')
for key in keys:
if key not in grp:
grp.create_group(key)
self.bai_1d.to_hdf5(grp['bai_1d'], compression)
self.bai_2d.to_hdf5(grp['bai_2d'], compression)
if not self.static:
self.mgi_1d.to_hdf5(grp['mgi_1d'], compression)
self.mgi_2d.to_hdf5(grp['mgi_2d'], compression)
def load_from_h5(self, replace=True, mode='r', *args, **kwargs):
"""Loads data stored in hdf5 file.
args:
data_only: bool, if True only loads the scan_data attribute
and does not load mg_args, bai_1d_args, or bai_2d_args.
set_mg: bool, if True instantiates the Multigeometry
object.
"""
with self.file_lock:
if replace:
self.reset()
with utils.catch_h5py_file(self.data_file, mode=mode) as file:
self._load_from_h5(file, *args, **kwargs)
def _load_from_h5(self, grp, data_only=False, set_mg=True):
"""Actual function for loading data, run with the file open and
holding the file_lock.
"""
with self.sphere_lock:
if 'type' in grp.attrs:
if grp.attrs['type'] == 'EwaldSphere':
for arch in grp['arches']:
if int(arch) not in self.arches.index:
self.arches.index.append(int(arch))
self.arches.sort_index(inplace=True)
if data_only:
lst_attr = [
"scan_data",
"overall_raw",
]
utils.h5_to_attributes(self, grp, lst_attr)
else:
lst_attr = [
"scan_data", "mg_args", "bai_1d_args",
"bai_2d_args", "overall_raw", "static", "gi",
"th_mtr", "single_img", "poni_dict"
]
utils.h5_to_attributes(self, grp, lst_attr)
self._set_args(self.bai_1d_args)
self._set_args(self.bai_2d_args)
if not self.static:
self._set_args(self.mg_args)
if "global_mask" in grp:
utils.h5_to_attributes(self, grp, ["global_mask"])
else:
self.global_mask = None
self.bai_1d.from_hdf5(grp['bai_1d'])
self.bai_2d.from_hdf5(grp['bai_2d'])
if not self.static:
self.mgi_1d.from_hdf5(grp['mgi_1d'])
self.mgi_2d.from_hdf5(grp['mgi_2d'])
if set_mg:
self.set_multi_geo(**self.mg_args)
def set_datafile(self,
fname,
name=None,
keep_current_data=False,
save_args={},
load_args={}):
"""Sets the data_file. If file exists and has data, loads in the
data. Otherwise, creates new file and resets self.
args:
fname: str, new data file
name: str or None, new name. If None, name is obtained from
fname.
keep_current_data: bool, if True overwrites any existing
data in the file. Otherwise, current data is either
overwritten by data in file or deleted if no data
exists, except any args dicts which are untouched.
save_args: dict, arguments to be passed to save_to_h5
load_args: dict, arguments to be passed to load_from_h5
"""
with self.sphere_lock:
self.data_file = fname
if name is None:
self.name = os.path.split(fname)[-1].split('.')[0]
else:
self.name = name
if keep_current_data:
self.save_to_h5(replace=True, **save_args)
else:
if os.path.exists(fname):
self.load_from_h5(replace=True, **load_args)
else:
self.reset()
self.save_to_h5(replace=True, **save_args)
def save_bai_1d(self, compression='lzf'):
"""Function to save only the bai_1d object.
args:
compression: str, what compression algorithm to pass to
h5py. See h5py documentation for acceptable compression
algorithms.
"""
compression = None
if self.static:
compression = None
with self.file_lock:
with utils.catch_h5py_file(self.data_file, 'a') as file:
self.bai_1d.to_hdf5(file['bai_1d'], compression=compression)
def save_bai_2d(self, compression='lzf'):
"""Function to save only the bai_2d object.
args:
compression: str, what compression algorithm to pass to
h5py. See h5py documentation for acceptable compression
algorithms.
"""
compression = None
if self.static:
compression = None
with self.file_lock:
with utils.catch_h5py_file(self.data_file, 'a') as file:
self.bai_2d.to_hdf5(file['bai_2d'], compression=compression)
def _set_args(self, args):
"""Ensures any range args are lists.
"""
for arg in args:
if 'range' in arg:
if args[arg] is not None:
args[arg] = list(args[arg])
class EwaldSphere(PawsPlugin):
"""Class for storing multiple arch objects, and stores a MultiGeometry
integrator from pyFAI.
Attributes:
name: str, name of the sphere
arches: Series, list of arches indexed by their idx value
data_file: str, file to save data to
scan_data: DataFrame, stores all scan metadata
mg_args: arguments for MultiGeometry constructor
multi_geo: MultiGeometry instance
bai_1d_args: dict, arguments for invidivual arch integrate1d method
bai_2d_args: not implemented
mgi_1d_I: array, intensity from MultiGeometry based integration
mgi_1d_2theta: array, two theta from MultiGeometry based integration
mgi_1d_q: array, q data from MultiGeometry based integration
mgi_2d_I: not implemented
mgi_2d_2theta: not implemented
mgi_2d_q: not implemented
file_lock: lock for ensuring one writer to hdf5 file
sphere_lock: lock for modifying data in sphere
bai_1d: int_1d_data object for by-arch integration
bai_2d: not implemented
Methods:
add_arch: adds new arch and optionally updates other data
by_arch_integrate_1d: integrates each arch individually and sums them
set_multi_geo: sets the MultiGeometry instance
multigeometry_integrate_1d: wrapper for MultiGeometry integrate1d
method
save_to_h5: saves data to hdf5 file
load_from_h5: loads data from hdf5 file
"""
def __init__(self,
name='scan0',
arches=[],
data_file='scan0',
scan_data=pd.DataFrame(),
mg_args={'wavelength': 1e-10},
bai_1d_args={},
bai_2d_args={}):
# TODO: add docstring for init
super().__init__()
self.name = name
if arches:
self.arches = pd.Series(arches, index=[a.idx for a in arches])
else:
self.arches = pd.Series()
self.data_file = data_file
self.scan_data = scan_data
self.mg_args = mg_args
self.multi_geo = MultiGeometry([a.integrator for a in arches],
**mg_args)
self.bai_1d_args = bai_1d_args
self.bai_2d_args = bai_2d_args
self.mgi_1d_I = 0
self.mgi_1d_2theta = 0
self.mgi_1d_q = 0
self.mgi_2d_I = 0
self.mgi_2d_2theta = 0
self.mgi_2d_q = 0
self.file_lock = Condition()
self.sphere_lock = Condition()
self.bai_1d = int_1d_data()
self.bai_2d = int_2d_data()
def add_arch(self,
arch=None,
calculate=True,
update=True,
get_sd=True,
set_mg=True,
**kwargs):
"""Adds new arch to sphere.
args:
arch: EwaldArch instance, arch to be added. Recommended to always
pass a copy of an arch with the arch.copy method
calculate: whether to run the arch's calculate methods after adding
update: bool, if True updates the bai_int attribute
get_sd: bool, if True tries to get scan data from arch
set_mg: bool, if True sets the MultiGeometry attribute. Takes a
long time, especially with longer lists. Recommended to run
set_multi_geo method after all arches are loaded.
returns None
"""
with self.sphere_lock:
if arch is None:
arch = EwaldArch(**kwargs)
if calculate:
arch.integrate_1d(**self.bai_1d_args)
# arch.integrate_2d(**self.bai_2d_args)
arch.file_lock = self.file_lock
self.arches = self.arches.append(pd.Series(arch, index=[arch.idx]))
self.arches.sort_index(inplace=True)
if arch.scan_info and get_sd:
ser = pd.Series(arch.scan_info, dtype='float64')
if list(self.scan_data.columns):
try:
self.scan_data.loc[arch.idx] = ser
except ValueError:
print('Mismatched columns')
else:
self.scan_data = pd.DataFrame(arch.scan_info,
index=[arch.idx],
dtype='float64')
self.scan_data.sort_index(inplace=True)
if update:
self._update_bai_1d(arch)
# self._update_bai_2d(arch)
if set_mg:
self.multi_geo = MultiGeometry(
[a.integrator for a in self.arches], **self.mg_args)
def by_arch_integrate_1d(self, **args):
"""Integrates all arches individually, then sums the results for
the overall integration result.
args: see EwaldArch.integrate_1d
"""
if not args:
args = self.bai_1d_args
else:
self.bai_1d_args = args.copy()
with self.sphere_lock:
self.bai_1d = int_1d_data()
for arch in self.arches:
arch.integrate_1d(**args)
self._update_bai_1d(arch)
def _update_bai_1d(self, arch):
"""helper function to update overall bai variables.
"""
self.bai_1d.raw += arch.int_1d.raw
self.bai_1d.pcount += arch.int_1d.pcount
self.bai_1d.norm = pawstools.div0(self.bai_1d.raw, self.bai_1d.pcount)
self.bai_1d.ttheta = arch.int_1d.ttheta
self.bai_1d.q = arch.int_1d.q
def set_multi_geo(self, **args):
"""Sets the MultiGeometry instance stored in the arch.
args: see pyFAI.multiple_geometry.MultiGeometry
"""
with self.sphere_lock:
self.multi_geo = MultiGeometry([a.integrator for a in self.arches],
**args)
self.mg_args = args
def multigeometry_integrate_1d(self, monitor=None, **kwargs):
"""Wrapper for integrate1d method of MultiGeometry.
args:
monitor: channel with normalization value
kwargs: see MultiGeometry.integrate1d
returns:
result: result from MultiGeometry.integrate1d
"""
with self.sphere_lock:
lst_mask = [a.mask for a in self.arches]
if monitor is None:
try:
result = self.multi_geo.integrate1d(
[a.map_norm for a in self.arches],
lst_mask=lst_mask,
**kwargs)
except Exception as e:
print(e)
result = self.multi_geo.integrate1d(
[a.map_raw for a in self.arches],
lst_mask=lst_mask,
**kwargs)
else:
result = self.multi_geo.integrate1d(
[a.map_raw for a in self.arches],
lst_mask=lst_mask,
normalization_factor=list(self.scan_data[monitor]),
**kwargs)
self.mgi_1d_I = result.intensity
self.mgi_1d_2theta, self.mgi_1d_q = parse_unit(
result, self.multi_geo.wavelength)
return result
def save_to_h5(self, file, arches=None, data_only=False, replace=False):
"""Saves data to hdf5 file.
args:
file: h5py file or group object
"""
with self.file_lock:
if self.name in file:
if replace:
del (file[self.name])
grp = file.create_group(self.name)
grp.create_group('arches')
else:
grp = file[self.name]
if 'arches' not in grp:
grp.create_group('arches')
else:
grp = file.create_group(self.name)
grp.create_group('arches')
if arches is None:
for arch in self.arches:
arch.save_to_h5(grp['arches'])
else:
for arch in self.arches[list(
set(self.arches.index).intersection(set(arches)))]:
arch.save_to_h5(grp['arches'])
if data_only:
lst_attr = [
"scan_data", "mgi_1d_q", "mgi_1d_I", "mgi_2d_2theta",
"mgi_2d_q", "mgi_2d_I"
]
else:
lst_attr = [
"data_file", "scan_data", "mg_args", "bai_1d_args",
"bai_2d_args", "mgi_1d_2theta", "mgi_1d_q", "mgi_1d_I",
"mgi_2d_2theta", "mgi_2d_q", "mgi_2d_I"
]
pawstools.attributes_to_h5(self, grp, lst_attr)
for key in ('bai_1d', 'bai_2d'):
if key not in grp:
grp.create_group(key)
pawstools.attributes_to_h5(self.bai_1d, grp['bai_1d'])
pawstools.attributes_to_h5(self.bai_2d, grp['bai_2d'])
def load_from_h5(self, file):
"""Loads data from hdf5 file.
args:
file: h5py file or group object
"""
with self.file_lock:
with self.sphere_lock:
if self.name not in file:
print("No data can be found")
grp = file[self.name]
self.arches = pd.Series()
for key in grp['arches'].keys():
arch = EwaldArch(idx=int(key))
arch.load_from_h5(grp['arches'])
self.add_arch(arch.copy(),
calculate=False,
update=False,
get_sd=False,
set_mg=False)
lst_attr = [
"data_file", "scan_data", "mg_args", "bai_1d_args",
"bai_2d_args", "mgi_1d_2theta", "mgi_1d_q", "mgi_1d_I",
"mgi_2d_2theta", "mgi_2d_q", "mgi_2d_I"
]
pawstools.h5_to_attributes(self, grp, lst_attr)
pawstools.h5_to_attributes(self.bai_1d, grp['bai_1d'])
pawstools.h5_to_attributes(self.bai_2d, grp['bai_2d'])
self.set_multi_geo(**self.mg_args)
def plot_100k(files,
centerx,
centery,
sdd,
name,
wavelength=.992e-10,
Qchidir='./plots/'):
"""
Return Q,I and save the Q-Chi plot to Qchidir.
Takes a list of filenames (use find_scans), centerx and centery, the sdd (in meters),
wavelength (in meters), sample name, and the directory to save a Q-chi image.
"""
import pyFAI
from pyFAI.multi_geometry import MultiGeometry
from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
# Check this is right? The mono energy should be in the spec file (no filetype)
w1 = wavelength
# Create a new detector. You should also be able to import the pilatus 100k from pyFAI.detectors
# but be careful, this has the angles defined differently (i.e.: positive tth = negative rot2)
det = pyFAI.detectors.Detector(172e-6, 172e-6)
det.max_shape = (487, 195)
poni1 = (487 - centerx) * 172e-6
poni2 = centery * 172e-6
# Define ai for scan 1
ai = pyFAI.AzimuthalIntegrator(dist=sdd,
poni1=poni1,
poni2=poni2,
detector=det)
ai.set_wavelength(w1)
# If you want to play with tilts, set the initial ai.rot1, rot2, rot3 here.
ai.rot1 = 0 * np.pi / 180
ai.rot2 = -6 * np.pi / 180
ai.rot3 = 0 * np.pi / 180
imgs = []
ais = []
step = 1 * np.pi / 180
# For each scan, move rot2 and create a new ai using deepcopy
for i in range(54):
fn = files[i]
img = read_raw_100k(fn)
my_ai = deepcopy(ai)
my_ai.rot2 -= i * step
imgs.append(img)
ais.append(my_ai)
if i == 5: plt.imshow(img, origin='lower')
mg = MultiGeometry(ais, unit="q_A^-1", radial_range=(0.5, 5))
Q, I = mg.integrate1d(imgs, 5000)
# This creates and plots a Q-chi image
sns.set_style("white")
I2D, Q2D, chi = mg.integrate2d(imgs, 1000, 360)
fig2 = plt.figure(figsize=(10, 6))
plt.imshow(I2D[245:295],
origin="lower",
extent=[Q2D.min(), Q2D.max(), 0,
chi.max()],
aspect='auto',
cmap='hot')
plt.xlabel('Q / $\\AA ^{-1}$', fontsize=20)
plt.tick_params(axis='x', which='major', labelsize=16)
plt.ylabel('chi / $\\AA ^{-1}$', fontsize=20)
plt.tick_params(axis='y', which='major', labelsize=16)
plt.xlim(0.5, 2.5)
plt.title("{} Q vs chi".format(name), fontsize=24)
figname = "{}_Q_chi.png".format(name)
plt.savefig(Qchidir + figname)
plt.close(fig2)
return Q, I