diff --git a/src/TZPGcalc/GeoBeams.py b/src/TZPGcalc/GeoBeams.py
index f0fc76a659bf3eda1a90a651af9dd021a68badd6..e1e975256ce4c4062bf1632843cbe1644e132205 100644
--- a/src/TZPGcalc/GeoBeams.py
+++ b/src/TZPGcalc/GeoBeams.py
@@ -30,7 +30,8 @@ class GeoBeams:
'dVFM': -2, # Vertical Focusing Mirror position
'fVFM': 5.05, # VFM focal length
'dBOZ': -0.23, # Beam splitting Off axis Zone plate position
- 'fBOZ': 0.25, # BOZ focal length
+ 'fBOZ_x': 0.25, # BOZ horizontal focal length
+ 'fBOZ_y': 0.25, # BOZ vertical focal distance
'theta_grating': 0, # grating deflection angle in rad
'dSAMZ': 0.0, # Sample position
'WH': 0.8e-3, # BOZ horizontal width
@@ -55,7 +56,7 @@ class GeoBeams:
position x2, given the source position at x1.
"""
dEX, dIHF, dVFM, dHFM, dBOZ = symbols('dEX, dIHF, dVFM, dHFM, dBOZ')
- fVFM, fHFM, fBOZ = symbols('fVFM, fHFM, fBOZ')
+ fVFM, fHFM, fBOZ_x, fBOZ_y = symbols('fVFM, fHFM, fBOZ_x, fBOZ_y')
x1, theta1_x, x2 = symbols('x1, theta1_x, x2')
y1, theta1_y, y2 = symbols('y1, theta1_y, y2')
@@ -71,8 +72,8 @@ class GeoBeams:
self.VFM_f = lambdify(self.elems.keys(), self.VFM, ['numpy'])
# beams for the zone plate first order (0th order is unfocused)
- self.HBOZ = simplify(ThinLens(fBOZ)*self.HFM)
- self.VBOZ = simplify(ThinLens(fBOZ)*self.VFM)
+ self.HBOZ = simplify(ThinLens(fBOZ_x)*self.HFM)
+ self.VBOZ = simplify(ThinLens(fBOZ_y)*self.VFM)
self.HBOZ_f = lambdify(self.elems.keys(), self.HBOZ, ['numpy'])
self.VBOZ_f = lambdify(self.elems.keys(), self.VBOZ, ['numpy'])
@@ -105,7 +106,7 @@ class GeoBeams:
x += [ray[0].evalf()]
# BOZ
- ray = (ThinLens(self.elems['fBOZ']) *
+ ray = (ThinLens(self.elems['fBOZ_x']) *
FreeSpace(-self.elems['dHFM'] + self.elems['dBOZ'])*ray)
z_x += [self.elems['dBOZ']]
x += [ray[0].evalf()]
@@ -132,7 +133,7 @@ class GeoBeams:
y += [ray[0].evalf()]
# BOZ
- ray = (ThinLens(self.elems['fBOZ']) *
+ ray = (ThinLens(self.elems['fBOZ_y']) *
FreeSpace(-self.elems['dVFM']+self.elems['dBOZ'])*ray)
z_y += [self.elems['dBOZ']]
y += [ray[0].evalf()]
diff --git a/src/TZPGcalc/TZPGcalc.py b/src/TZPGcalc/TZPGcalc.py
index ff0fb2c6885fef26a8fb39c7216428825a2e368c..cf6a17d1ed24101938849d350e74e156864cbe4d 100644
--- a/src/TZPGcalc/TZPGcalc.py
+++ b/src/TZPGcalc/TZPGcalc.py
@@ -10,8 +10,9 @@
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
-from matplotlib.patches import Rectangle, Polygon
+from matplotlib.patches import PathPatch, Rectangle, Polygon
from matplotlib.colors import hsv_to_rgb
+from matplotlib.path import Path
import ipywidgets as widgets
from ipywidgets import HBox, VBox
@@ -31,7 +32,9 @@ TZPG_db = {
'TZPGwV': 1,
'TZPGoffaxis': 0.75,
'grating': 3.8,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
},
'O': {
'design_nrj': 530,
@@ -39,7 +42,9 @@ TZPG_db = {
'TZPGwV': 0.8,
'TZPGoffaxis': 0.55,
'grating': 3.1,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
},
'Fe': {
'design_nrj': 715,
@@ -47,7 +52,9 @@ TZPG_db = {
'TZPGwV': 0.8,
'TZPGoffaxis': 0.55,
'grating': 3.1,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
},
'Co': {
'design_nrj': 785,
@@ -55,7 +62,9 @@ TZPG_db = {
'TZPGwV': 0.8,
'TZPGoffaxis': 0.55,
'grating': 3.1,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
},
'Ni': {
'design_nrj': 860,
@@ -63,7 +72,9 @@ TZPG_db = {
'TZPGwV': 0.8,
'TZPGoffaxis': 0.55,
'grating': 3.1,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
},
'Cu': {
'design_nrj': 927,
@@ -71,7 +82,9 @@ TZPG_db = {
'TZPGwV': 0.8,
'TZPGoffaxis': 0.55,
'grating': 3.1,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
},
'Gd': {
'design_nrj': 1210,
@@ -79,7 +92,9 @@ TZPG_db = {
'TZPGwV': 0.8,
'TZPGoffaxis': 0.55,
'grating': 3.1,
- 'F': 0.25
+ 'F_x': 0.25,
+ 'F_y': 0.25,
+ '3beams': True
}
}
@@ -87,14 +102,9 @@ TZPG_db = {
class TZPGcalc():
def __init__(self):
self.geo_beams = GeoBeams()
- self.initFig()
self.initWidgets()
- for v in ['fVFM', 'fHFM', 'EXw', 'IHFw']:
- if v in ['fVFM', 'fHFM']:
- scale = 1.0
- else:
- scale = 1e6
- self.widgets[v].value = scale*self.geo_beams.elems[v]
+ self.initFig()
+ self.init_beam_transport()
# spot sizes of all beams
self.SpotSizes = {}
@@ -106,6 +116,16 @@ class TZPGcalc():
self.UpdateFig()
display(self.control)
+ def init_beam_transport(self):
+ temp = GeoBeams()
+ # set default value for beam transport
+ for v in ['fVFM', 'fHFM', 'EXw', 'IHFw']:
+ if v in ['fVFM', 'fHFM']:
+ scale = 1.0
+ else:
+ scale = 1e6
+ self.widgets[v].value = scale*temp.elems[v]
+
def initFig(self):
"Creates a figure for the sample plane and detector plane images."
@@ -204,7 +224,7 @@ class TZPGcalc():
angle=45))
}
- # 5x5 membranes
+ # SampleNxSampleN membranes
self.sampleLines = {}
self.etchLines = {}
for k in range(SampleN*SampleN):
@@ -214,6 +234,63 @@ class TZPGcalc():
Rectangle((0, 0), 1, 1, fill=False, facecolor='k',
alpha=0.4, ls='--'))
+ # Flat Liquid Jet
+ self.FLJ_lines = {}
+ self.FlatLiquidJet()
+
+ def FlatLiquidJet(self):
+ """Draw a Flat Liquid jet.
+ """
+ sw = self.widgets
+ HW = 0.5*sw['FLJ_W'].value # [mm]
+ L = sw['FLJ_L'].value # [mm]
+ mf = sw['FLJ_mf'].value # [mm]
+ incidence = np.deg2rad(sw['samIncidence'].value) # [rad]
+ ox = sw['samX'].value # [mm]
+ oy = -L/2 + sw['samY'].value # [mm]
+
+ # incidence angle squeezes sample
+ ci = np.cos(incidence)
+
+ verts = [
+ [(0*ci, L + oy), # P0
+ (HW/2*ci, L + oy), # P1
+ (HW*ci, 0.5*(1+mf)*L + oy), # P2
+ (HW*ci, mf*L + oy)], # P3
+ [(HW*ci, mf*L + oy), # P0
+ (HW*ci, 0.5*mf*L + oy), # P1
+ (0, 0 + oy), # P2
+ (0, 0 + oy)] # P3
+ ]
+
+ # second half image of liquid jet
+ mirror = []
+ for v in verts:
+ mirror.append([(-p[0], p[1]) for p in v])
+
+ verts += mirror
+
+ # apply offsets
+ fverts = []
+ for v in verts:
+ fverts.append([(p[0] + ox, p[1]) for p in v])
+
+ codes = [
+ Path.MOVETO, # P0
+ Path.CURVE4, # P1
+ Path.CURVE4, # P2
+ Path.CURVE4 # P3
+ ]
+
+ for k, v in enumerate(fverts):
+ path = Path(v, codes)
+ if k in self.FLJ_lines:
+ self.FLJ_lines[k].remove()
+
+ self.FLJ_lines[k] = self.ax_sam.add_patch(
+ PathPatch(path, alpha=0.4, facecolor='none', lw=2)
+ )
+
def RectUpdate(self, rect, xLeft, yBottom, xRight, yTop):
"""Updates the position and size of the given Rectangle.
@@ -266,7 +343,8 @@ class TZPGcalc():
# shortcut
sge = self.geo_beams.elems
- sge['fBOZ'] = conf['F']
+ sge['fBOZ_x'] = conf['F_x']
+ sge['fBOZ_y'] = conf['F_y']
sge['theta_grating'] = conf['theta_grating']
# imaging plane
@@ -290,6 +368,11 @@ class TZPGcalc():
self.SpotSizes[img['type']][conf['Energy']][z, k] = (
1e3*(np.max(vs) - np.min(vs)))
+ # 3 beams configuration
+ b = self.widgets['3beams'].value
+ Beams['F0G0'].set_visible(b)
+ Beams['F1G0'].set_visible(b)
+
def DetectorUpdate(self, Xoff, Yoff):
"""Draws DSSC detector module with filter mask.
@@ -325,8 +408,28 @@ class TZPGcalc():
self.detLines['diamond'].set_xy((
self.scale*Xoff, self.scale*(Yoff - diamondW/2*np.sqrt(2))))
- def SampleUpdate(self, w, p, Xoff, Yoff, thickness=0.525,
- incidence=0, etch_angle=54.74):
+ def SampleUpdate(self):
+ if self.widgets['SampleType'].value == 'Membranes Array':
+ b = True
+ elif self.widgets['SampleType'].value == 'Flat Liquid Jet':
+ b = False
+ else:
+ raise ValueError('Sample type must be either "Membranes Array" or'
+ '"Flat Liquid Jet"')
+
+ for k in range(SampleN*SampleN):
+ self.sampleLines[k].set_visible(b)
+ self.etchLines[k].set_visible(b)
+
+ for k in range(4):
+ self.FLJ_lines[k].set_visible(not(b))
+
+ if b:
+ self.MembraneSampleUpdate()
+ else:
+ self.FlatLiquidJet()
+
+ def MembraneSampleUpdate(self):
"""Draws the sample.
Inputs
@@ -339,6 +442,15 @@ class TZPGcalc():
incidence: incidence angle in rad
etch_angle: etching angle from surface in rad
"""
+ sw = self.widgets
+ w = sw['samw'].value*1e-3 # [m]
+ p = sw['samp'].value*1e-3 # [m]
+ Xoff = sw['samX'].value*1e-3 # [m]
+ Yoff = sw['samY'].value*1e-3 # [m]
+ thickness = sw['samthickness'].value*1e-6 # [m]
+ etch_angle = np.deg2rad(sw['samEtchAngle'].value) # [rad]
+ incidence = np.deg2rad(sw['samIncidence'].value) # [rad]
+
# Si etching angle
wp = w + 2*thickness/np.tan(etch_angle)
@@ -371,12 +483,13 @@ class TZPGcalc():
# we calculate the optics for the central wavelength
nrjL = sw['nrjL'].value # [eV]
nrjH = sw['nrjH'].value # [eV]
+ nrjD = sw['nrjD'].value # [eV]
wlL = 1240/nrjL*1e-9
wlH = 1240/nrjH*1e-9
- nrjD = sw['nrjD'].value # [eV]
wlD = 1240/nrjD*1e-9
- F = sw['F'].value # [m] hidden nominal focal length
+ F_x = sw['F_x'].value # [m] Nominal horiz. BOZ focal length
+ F_y = sw['F_y'].value # [m] Nominal vert. BOZ focal length
theta_grating = sw['grating'].value*1e-3 # [rad]
sampleZ = sw['SAMZ'].value*1e-3 # [m]
samIncidence = np.deg2rad(sw['samIncidence'].value) # [rad]
@@ -397,21 +510,30 @@ class TZPGcalc():
# zone plate radius at the point further away from the optical axis
rn = np.sqrt((sge['WH']/2.0)**2 +
(sge['WV']/2.0 + np.abs(sge['offaxis']))**2)
- dr_nominal = wlD * F / (2*rn)
- sw['dr_label'].value = (
- f'Outer Zone Plate width dr:{int(np.round(dr_nominal*1e9))} nm')
+ dr_nominal_x = wlD * F_x / (2*rn)
+ dr_nominal_y = wlD * F_y / (2*rn)
+ sw['dr_label_x'].value = (
+ f'Outer Zone Plate width dr for Horiz. '
+ f'focus:{int(np.round(dr_nominal_x*1e9))} nm')
+ sw['dr_label_y'].value = (
+ f'for Vert. focus:{int(np.round(dr_nominal_y*1e9))} nm')
# Optics properties (focal length and grating angle) for the
# low energy and high energy photon
- F_L = 2*rn*dr_nominal/wlL
+ F_L_x = 2*rn*dr_nominal_x/wlL
+ F_L_y = 2*rn*dr_nominal_y/wlL
G_L = np.arcsin(wlL/d_nominal)
confL = {'Energy': 'L',
- 'F': F_L,
+ 'F_x': F_L_x,
+ 'F_y': F_L_y,
'theta_grating': G_L}
- F_H = 2*rn*dr_nominal/wlH
+
+ F_H_x = 2*rn*dr_nominal_x/wlH
+ F_H_y = 2*rn*dr_nominal_y/wlH
G_H = np.arcsin(wlH/d_nominal)
confH = {'Energy': 'H',
- 'F': F_H,
+ 'F_x': F_H_x,
+ 'F_y': F_H_y,
'theta_grating': G_H}
# Configuration for imaging plane
@@ -439,14 +561,7 @@ class TZPGcalc():
self.DetectorUpdate(detXoff, detYoff)
# update the sample
- samw = self.widgets['samw'].value*1e-3 # [m]
- samp = self.widgets['samp'].value*1e-3 # [m]
- samXoff = self.widgets['samX'].value*1e-3 # [m]
- samYoff = self.widgets['samY'].value*1e-3 # [m]
- samthickness = self.widgets['samthickness'].value*1e-6 # [m]
- samEtchAngle = np.deg2rad(self.widgets['samEtchAngle'].value) # [rad]
- self.SampleUpdate(samw, samp, samXoff, samYoff, samthickness,
- samIncidence, samEtchAngle)
+ self.SampleUpdate()
def initWidgets(self):
""" Creates the necessary interactive widget controls.
@@ -476,6 +591,14 @@ class TZPGcalc():
])
# Source
+ self.Reset = widgets.Button(
+ description='Reset',
+ )
+
+ @self.Reset.on_click
+ def reset_on_click(b):
+ self.init_beam_transport()
+
self.widgets['EXw'] = widgets.BoundedIntText(
value=100,
min=0,
@@ -513,6 +636,7 @@ class TZPGcalc():
layout=layout
)
SourceTab = VBox([
+ self.Reset,
self.widgets['EXw'],
self.widgets['IHFw'],
self.widgets['fVFM'],
@@ -534,17 +658,33 @@ class TZPGcalc():
self.widgets['TZPGwV'].value = v['TZPGwV']
self.widgets['TZPGoffaxis'].value = v['TZPGoffaxis']
self.widgets['grating'].value = v['grating']
- self.widgets['F'].value = v['F']
+ self.widgets['F_x'].value = v['F_x']
+ self.widgets['F_y'].value = v['F_y']
+ self.widgets['3beams'].value = v['3beams']
+
# necessary to recompute grating pitch and outer zone plate width
self.UpdateFig()
self.widgets['Type'].observe(TZPGtype, names='value')
# hidden nominal zone plate focus
- self.widgets['F'] = widgets.BoundedFloatText(
+ self.widgets['F_x'] = widgets.BoundedFloatText(
value=0.25,
min=0,
- max=1
+ max=1,
+ step=0.01,
+ description='Focal length (m) Horiz.:',
+ style=style,
+ layout=layout
+ )
+ self.widgets['F_y'] = widgets.BoundedFloatText(
+ value=0.25,
+ min=0,
+ max=1,
+ step=0.01,
+ description='Vert.:',
+ style=style,
+ layout=layout
)
self.widgets['nrjL'] = widgets.BoundedIntText(
@@ -571,7 +711,7 @@ class TZPGcalc():
max=3200,
step=1,
width=4,
- description='Design:',
+ description='Design energy (eV):',
style=style,
layout=layout
)
@@ -611,15 +751,26 @@ class TZPGcalc():
style=style,
layout=layout
)
- self.widgets['dr_label'] = widgets.Label(value='dr')
+ self.widgets['3beams'] = widgets.Checkbox(
+ value=True,
+ description='3 beams:',
+ style=style,
+ layout=layout
+ )
+ self.widgets['dr_label_x'] = widgets.Label(value='dr_x')
+ self.widgets['dr_label_y'] = widgets.Label(value='dr_y')
self.widgets['d_label'] = widgets.Label(value='dr')
TZPGTab = VBox([
self.widgets['Type'],
HBox([self.widgets['nrjD'],
- self.widgets['grating'],
- self.widgets['TZPGoffaxis']]),
- HBox([self.widgets['d_label'],
- self.widgets['dr_label']]),
+ self.widgets['F_x'],
+ self.widgets['F_y']
+ ]),
+ HBox([self.widgets['grating'],
+ self.widgets['TZPGoffaxis'],
+ self.widgets['3beams']]),
+ HBox([self.widgets['dr_label_x'],
+ self.widgets['dr_label_y']]),
HBox([widgets.Label(value='Energy range (eV):'),
self.widgets['nrjL'], self.widgets['nrjH']]),
HBox([widgets.Label(value='TZPG (mm):'),
@@ -628,6 +779,13 @@ class TZPGcalc():
])
# sample part
+ self.widgets['SampleType'] = widgets.Dropdown(
+ options=['Membranes Array', 'Flat Liquid Jet'],
+ value='Membranes Array',
+ decription='Sample type:',
+ style=style,
+ layout=layout
+ )
self.widgets['SAMZ'] = widgets.BoundedFloatText(
value=30.,
min=-10.,
@@ -637,12 +795,14 @@ class TZPGcalc():
style=style,
layout=layout
)
+
+ # membranes
self.widgets['samw'] = widgets.BoundedFloatText(
value=.5,
min=0.01,
max=2.0,
step=.01,
- description='width:',
+ description='width (mm):',
style=style,
layout=layout
)
@@ -651,10 +811,58 @@ class TZPGcalc():
min=0.01,
max=2.0,
step=.01,
- description='pitch:',
+ description='pitch (mm):',
+ style=style,
+ layout=layout
+ )
+ self.widgets['samthickness'] = widgets.BoundedFloatText(
+ value=381,
+ min=1,
+ max=1000,
+ step=1,
+ description='Substrate thickness (um):',
+ style=style,
+ layout=layout
+ )
+ self.widgets['samEtchAngle'] = widgets.BoundedFloatText(
+ value=54.74,
+ min=0,
+ max=90,
+ step=0.01,
+ description='etch angle (deg):',
+ style=style,
+ layout=layout
+ )
+
+ # Flat Liquid Jet
+ self.widgets['FLJ_W'] = widgets.BoundedFloatText(
+ value=1.0,
+ min=0,
+ max=5,
+ step=0.1,
+ description='Flat Liquid Jet width (mm):',
+ style=style,
+ layout=layout
+ )
+ self.widgets['FLJ_L'] = widgets.BoundedFloatText(
+ value=4.6,
+ min=0,
+ max=15,
+ step=0.1,
+ description='of length (mm):',
style=style,
layout=layout
)
+ self.widgets['FLJ_mf'] = widgets.BoundedFloatText(
+ value=0.75,
+ min=0,
+ max=1,
+ step=0.01,
+ description='at:',
+ style=style,
+ layout=layout
+ )
+
self.widgets['samX'] = widgets.BoundedFloatText(
value=0.,
min=-10,
@@ -673,15 +881,6 @@ class TZPGcalc():
style=style,
layout=layout
)
- self.widgets['samthickness'] = widgets.BoundedFloatText(
- value=381,
- min=1,
- max=1000,
- step=1,
- description='Substrate thickness (um):',
- style=style,
- layout=layout
- )
self.widgets['samIncidence'] = widgets.BoundedFloatText(
value=0,
min=0,
@@ -691,26 +890,22 @@ class TZPGcalc():
style=style,
layout=layout
)
- self.widgets['samEtchAngle'] = widgets.BoundedFloatText(
- value=54.74,
- min=0,
- max=90,
- step=0.01,
- description='Etch angle from surface (deg):',
- style=style,
- layout=layout
- )
samTab = VBox([
self.widgets['SAMZ'],
- HBox([widgets.Label(value='Membrane (mm), '),
+ self.widgets['SampleType'],
+ HBox([widgets.Label(value='Membranes array, '),
self.widgets['samw'],
self.widgets['samp']]),
+ HBox([self.widgets['samthickness'],
+ self.widgets['samEtchAngle']]),
+ HBox([self.widgets['FLJ_W'],
+ self.widgets['FLJ_mf'],
+ self.widgets['FLJ_L']]),
HBox([widgets.Label(value='Sample Offset (mm), '),
self.widgets['samX'],
self.widgets['samY']]),
- self.widgets['samthickness'],
HBox([self.widgets['samIncidence'],
- self.widgets['samEtchAngle']])
+ ])
])
# Detector tab
@@ -724,7 +919,7 @@ class TZPGcalc():
layout=layout
)
self.widgets['detX'] = widgets.BoundedFloatText(
- value=20.,
+ value=34.5,
min=-50,
max=50,
step=0.5,
@@ -733,7 +928,7 @@ class TZPGcalc():
layout=layout
)
self.widgets['detY'] = widgets.BoundedFloatText(
- value=0.,
+ value=-2.,
min=-50,
max=50,
step=0.5,