def propagate_NVE():
wfr_directory = sys.argv[1].replace("*", "/")
job_name = "NKB_4980eV_250pC_NVE_to_EHC"
python_command = propagate_NVE
input_directory = dCache + "/NanoKB-Pulse/NVE/"
save_directory = input_directory.replace("/NVE/", "/EHC/")
mkdir_p(save_directory)
log_directory = logs
focus = "nano"
analysis = False
filename = __file__
dt = datetime.now().__str__()
function = python_command.__name__
description = "Propagate NanoKB Pulses 4.98 keV, 250 pC from Undulator NVE mirror to the EHC Screen"
append = None
print("info")
print("wavefront directory: {}".format(wfr_directory))
print("save directory: {}".format(save_directory))
print("focus (i.e. beamline option): {}".format(focus))
print("analysis: {}".format(analysis))
print("datetime: {}".format(dt))
print("filename: {}".format(filename))
print("function: {}".format(function))
print("description: {}".format(description))
wfr = Wavefront()
wfr.load_hdf5(wfr_directory)
bl = Beamline()
bl.append(Drift(2.2+3.5), propagation_parameters(1/3,1,1/3,1,'quadratic'))
bl.propagate(wfr)
wfr.custom_fields['focus'] = focus
wfr.custom_fields['job name'] = job_name
wfr.custom_fields['input directory'] = wfr_directory
wfr.custom_fields['datetime'] = dt
wfr.custom_fields['function'] = function
wfr.custom_fields['filename'] = filename
wfr.custom_fields['description'] = description
#wfr.custom_fields['bl'] = bl.__str__
if analysis:
wfr.analysis()
wfr.store_hdf5(wfr_directory.replace("/NVE/", "/EHC/"))
def detect(self, wfr):
xMin, xMax, yMax, yMin = wfr.get_limits()
idx, idy = xMax-xMin, yMax-yMin
inx, iny = wfr.params.Mesh.nx, wfr.params.Mesh.ny
print(idx,idy)
print((self.dy*self.ny)/idy)
bl = Beamline()
bl.append(Drift(0),
propagation_parameters((self.dx*self.nx)/idx, self.nx/inx, (self.dy*self.ny)/idy, self.ny/iny))
bl.propagate(wfr)
def detect(self, wfr):
"""
return the detected intensity distribution
"""
bl = Beamline()
bl.append(
Drift(0),
propagation_parameters(self.mesh.dx / wfr.dx, 1,
self.mesh.dy / wfr.dy, 1))
bl.propagate(wfr)
ii = wfr.get_intensity().sum(-1)
ii = compress_and_average(ii, (self.mesh.nx, self.mesh.ny))
return ii
def add_screen(self, position, distance, screenName=None):
"""
add a screening plane at drift beyond some element position
:param position: last optical element before screen
:param distance: position from last optical element to screen
:param screenName: name of the screen element (ie., MKB-scr etc) [str]
"""
self.crop_beamline(element1=position)
drift2screen = Drift(distance)
if screenName is not None:
drift2screen.name = "screen"
else:
drift2screen.name = screenName
self.bl.append(Drift(distance),
propagation_parameters(1, 1, 1, 1, m='quadratic'))
def scale(self, wfr, iscx=1024, iscy=1024, ifov=800e-06):
"""
DEPR.
narrow functionality for scaling a wavefront (ie the number of pixels)
in the source plane
:param wfr: wpg wfr strucutre
:param isc: ideal scale
:param ifov: ideal field of view
:returns wfr: scaled wpg wfr structure
"""
nx, ny = wfr.params.Mesh.nx, wfr.params.Mesh.ny
dx, dy = wfr.params.Mesh.xMax - wfr.params.Mesh.xMin, wfr.params.Mesh.yMax - wfr.params.Mesh.yMin
scbl = Beamline()
scbl.append(
Aperture('r', 'a', 800e-06, 800e-06),
propagation_parameters(dx / ifov, iscx / nx, dy / ifov, iscy / ny))
scbl.propagate(wfr)
return wfr
src.store_hdf5("../data/tmp/source.h5")
except (KeyError):
os.remove("../data/tmp/source.h5")
src.store_hdf5("../data/tmp/source.h5")
src = Source()
src.load_hdf5("../data/tmp/source.h5")
from felpy.model.wavefront import Wavefront
from wpg.wpg_uti_wf import plot_intensity_map
wfr = Wavefront()
from felpy.model.beamline import Beamline
from wpg.optical_elements import Drift
from felpy.model.tools import propagation_parameters
from matplotlib import pyplot as plt
bl = Beamline()
bl.append(Drift(50), propagation_parameters(1, 1, 1, 1, mode='fresnel'))
for w in src.pulses:
wfr.load_hdf5(w)
bl.propagate(wfr)
plt.plot(wfr.x_axis,
wfr.get_x_profile(),
label="{} $\mu$ rad".format(wfr.source_properties['theta_x'] *
1e6))
#plot_intensity_map(wfr)
print(wfr.com)
plt.legend()
ny = 25
plt.imshow(create_mask(nx, ny))
wfr = construct_SA1_wavefront(512, 512, 5, .8, mx=0, xoff=0, tiltX=0)
period = nx * wfr.get_spatial_resolution()[0] * (512 / (nx))
print(period)
wav = wfr.get_wavelength()
d = (2 * period**2) / wav
arr = create_mask(nx, ny)
np.save("/opt/arr", arr)
im = Image.fromarray(arr)
im = im.convert('RGB')
im.save("/opt/arr.png")
obj = srwloptT("/opt/arr.png",
wfr.get_spatial_resolution()[0] * (512 / 75),
wfr.get_spatial_resolution()[1] * (512 / 75),
1e-06,
1e-8,
atten_len=1e-08)
bl = Beamline()
bl.append(Drift(50), propagation_parameters(1, 1, 1, 1, mode='quadratic'))
bl.append(obj, propagation_parameters(1, 1, 1, 1))
bl.append(Drift(d),
propagation_parameters(1 / 3, 4, 1 / 3, 4, mode='fraunhofer'))
bl.propagate(wfr)
plot_intensity_map(wfr)
def build_beamline(self, focus="nano", screens="false"):
"""
Construct the beamline object
:param focus: what beamline configuration (micron or nano)
"""
self.bl = Beamline()
if focus == "micron":
self.bl.append(
self.d1, propagation_parameters(1, 1, 1, 1, mode="fraunhofer"))
self.bl.append(self.HOM1,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d2, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.HOM2,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d3, propagation_parameters(1, 1, 1, 1, mode='fraunhofer'))
self.bl.append(
self.MKB_pslit,
propagation_parameters(1 / 5, 1, 1 / 5, 1, mode='fresnel'))
self.bl.append(
self.d4, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MHP,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d5, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MHE,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.MHE_error,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d6, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MVE,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.MVE_error,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d8, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MVP,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.df,
propagation_parameters(5, 1, 5, 1, mode='converge'))
elif focus == "nano":
self.bl.append(
self.d1, propagation_parameters(1, 1, 1, 1, mode="fraunhofer"))
self.bl.append(self.HOM1,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d2, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.HOM2,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d3, propagation_parameters(1, 1, 1, 1, mode='fraunhofer'))
self.bl.append(
self.NKB_pslit,
propagation_parameters(1 / 10, 1, 1 / 10, 1, mode='fresnel'))
self.bl.append(
self.d4, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.NHE_error,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.NHE,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d5, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.NVE_error,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.NVE,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.df,
propagation_parameters(1 / 20, 1, 1 / 20, 1, mode='converge'))
self.bl.params = self.params
def build_beamline(self, focus="nano", screens="false"):
"""
Construct the beamline object
:param focus: what beamline configuration (micron or nano)
"""
self.bl = Beamline()
if focus == 'direct':
self.bl.append(
self.d1, propagation_parameters(1, 1, 1, 1, mode="quadratic"))
self.bl.append(self.HOM1,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d2, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.HOM2,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d3, propagation_parameters(2, 1, 2, 1, mode='fraunhofer'))
self.bl.append(
self.NKB_PSlit,
propagation_parameters(1 / 10, 1, 1 / 10, 1, mode='fresnel'))
self.bl.append(
self.d4, propagation_parameters(1, 1, 1, 1, mode='fraunhofer'))
self.bl.append(
self.d5, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(
self.df, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
if focus == "micron":
self.bl.append(
self.d1, propagation_parameters(1, 1, 1, 1, mode="fraunhofer"))
self.bl.append(self.HOM1,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d2, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.HOM2,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d3, propagation_parameters(1, 1, 1, 1, mode='fraunhofer'))
self.bl.append(
self.d4, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MHP,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d5, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MHE,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.MHE_error,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d6, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MVE,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.MVE_error,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(
self.d8, propagation_parameters(1, 1, 1, 1, mode='quadratic'))
self.bl.append(self.MVP,
propagation_parameters(1, 1, 1, 1, mode='fresnel'))
self.bl.append(self.df,
propagation_parameters(5, 1, 5, 1, mode='converge'))
elif focus == "nano":
self.bl.append(self.d1,
propagation_parameters(*self.params['d1']['pp']))
self.bl.append(self.HOM1,
propagation_parameters(*self.params['HOM1']['pp']))
self.bl.append(self.d2,
propagation_parameters(*self.params['d2']['pp']))
self.bl.append(self.HOM2,
propagation_parameters(*self.params['HOM2']['pp']))
self.bl.append(self.d3,
propagation_parameters(*self.params['d3']['pp']))
self.bl.append(
self.NKB_PSlit,
propagation_parameters(*self.params['NKB_PSlit']['pp']))
self.bl.append(self.d4,
propagation_parameters(*self.params['d4']['pp']))
self.bl.append(
self.NHE_error,
propagation_parameters(*self.params['NHE_error']['pp']))
self.bl.append(self.NHE,
propagation_parameters(*self.params['NHE']['pp']))
self.bl.append(self.d5,
propagation_parameters(*self.params['d5']['pp']))
self.bl.append(
self.NVE_error,
propagation_parameters(*self.params['NVE_error']['pp']))
self.bl.append(self.NVE,
propagation_parameters(*self.params['NVE']['pp']))
#self.bl.append(self.df, propagation_parameters(1,1,1,1, mode = 'converge'))
#self.bl.append(self.df, propagation_parameters(15,1,15,1, mode = 'converge')) ### perfect mirrors
self.bl.params = self.params
# -*- coding: utf-8 -*-
import sys
from felpy.model.wavefront import Wavefront
from felpy.model.beamline import Beamline
from wpg.optical_elements import Drift
from felpy.model.tools import propagation_parameters
from felpy.utils.os_utils import mkdir_p
if __name__ == '__main__':
print("working")
in_directory = sys.argv[1]
print("in: ", in_directory)
out_directory = sys.argv[2]
print("out: ", out_directory)
wfr = Wavefront()
wfr.load_hdf5(in_directory)
print("wfr loaded")
bl = Beamline()
bl.append(Drift(3.644 - 2.2),
propagation_parameters(1, 1, 1, 1, 'quadratic'))
bl.propagate(wfr)
print("wfr propagated")
wfr.store_hdf5(out_directory)
print("wfr stored")
wfr.analysis(VERBOSE=True, DEBUG=True)
#print(wfr.custom_fields) ## good debug
print(oe)
srwl.PropagElecField(wfr._srwl_wf, bl)
if return_intensity:
intensity.append(wfr.get_intensity().sum(-1))
if return_mesh:
mesh.append(wfr.get_mesh())
plot_intensity_map(wfr)
if return_intensity:
if return_mesh:
return intensity, mesh
else:
return intensity
if __name__ == '__main__':
from felpy.model.src.coherent import construct_SA1_pulse
from felpy.model.tools import propagation_parameters
from wpg.optical_elements import Drift
wfr = construct_SA1_pulse(512,512,2,5.0,1)
print(wfr.params.wDomain)
wfr.plot()
bl = Beamline()
bl.append(Drift(10), propagation_parameters(2,1,2,1,'quadratic'))
bl.propagate_sequential(wfr)
#
# =============================================================================
q = 0.50
src = construct_SA1_wavefront(1024, 1024, 25.0, q)
plot_ii(src)
speckle = define_speckle_mask("../../data/samples/checkerboard-pattern.jpg",
rx=1e-8,
ry=1e-8,
sample_thickness=150e-06,
sample_delta=4e-04,
plot=True,
ekev=25)
bl.append(Drift(10), propagation_parameters(1, 1, 1, 1, mode='quadratic'))
bl.append(speckle, propagation_parameters(1, 1, 1, 1, mode='fresnel'))
#plot_ii(src)
bl.append(Drift(z2),
propagation_parameters(1 / 4, 4, 1 / 4, 4, mode='quadratic'))
bl.propagate(src)
src.view()
# =============================================================================
# plot_ii(src)
#
# d = Detector(5e-07, 5e-07, 1024, 1024)
# d.detect(src)
# =============================================================================
plot_ii(src)
k = np.pi * 2 / wav
delta = 4e-07
d2waist = (wav) / (np.arctan(.27 / 8) * np.pi)
r = 75e-03
wfr = Wavefront(
construct_gaussian(1024, 1024, 25, -15e-02, 15e-02, -15e-02, 15e-02, 3e-2,
3e-02, d2waist))
### PLOT 1
plot_intensity_map(wfr)
bl = Beamline()
bl.append(Drift(1), propagation_parameters(1, 1, 1, 1))
bl.propagate(wfr)
x = np.linspace(wfr.params.Mesh.xMin, wfr.params.Mesh.xMax, wfr.params.Mesh.nx)
y = np.ones([wfr.params.Mesh.nx, wfr.params.Mesh.ny])
thickness = norm(cylinder_thickness(x, r, offset=0), lim=(0, 255))
sdir = "../../data/samples/cylinder_thickness.png"
im = Image.fromarray(thickness * y)
im = im.convert("L")
im.save(sdir)
np.save(sdir, thickness)
rx, ry = wfr.get_spatial_resolution()