From 0b7a068775c9a5aba471cf8e27abdba4a6bd344b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Le=20Guyader?= <loic.le.guyader@xfel.eu>
Date: Fri, 1 Oct 2021 17:06:14 +0200
Subject: [PATCH] Adds Flat liquid Jet
---
src/TZPGcalc/TZPGcalc.py | 236 +++++++++++++++++++++++++++++++--------
1 file changed, 190 insertions(+), 46 deletions(-)
diff --git a/src/TZPGcalc/TZPGcalc.py b/src/TZPGcalc/TZPGcalc.py
index 74e4dcb..cf6a17d 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
@@ -32,7 +33,8 @@ TZPG_db = {
'TZPGoffaxis': 0.75,
'grating': 3.8,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
},
'O': {
'design_nrj': 530,
@@ -41,7 +43,8 @@ TZPG_db = {
'TZPGoffaxis': 0.55,
'grating': 3.1,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
},
'Fe': {
'design_nrj': 715,
@@ -50,7 +53,8 @@ TZPG_db = {
'TZPGoffaxis': 0.55,
'grating': 3.1,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
},
'Co': {
'design_nrj': 785,
@@ -59,7 +63,8 @@ TZPG_db = {
'TZPGoffaxis': 0.55,
'grating': 3.1,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
},
'Ni': {
'design_nrj': 860,
@@ -68,7 +73,8 @@ TZPG_db = {
'TZPGoffaxis': 0.55,
'grating': 3.1,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
},
'Cu': {
'design_nrj': 927,
@@ -77,7 +83,8 @@ TZPG_db = {
'TZPGoffaxis': 0.55,
'grating': 3.1,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
},
'Gd': {
'design_nrj': 1210,
@@ -86,7 +93,8 @@ TZPG_db = {
'TZPGoffaxis': 0.55,
'grating': 3.1,
'F_x': 0.25,
- 'F_y': 0.25
+ 'F_y': 0.25,
+ '3beams': True
}
}
@@ -94,8 +102,8 @@ TZPG_db = {
class TZPGcalc():
def __init__(self):
self.geo_beams = GeoBeams()
- self.initFig()
self.initWidgets()
+ self.initFig()
self.init_beam_transport()
# spot sizes of all beams
@@ -216,7 +224,7 @@ class TZPGcalc():
angle=45))
}
- # 5x5 membranes
+ # SampleNxSampleN membranes
self.sampleLines = {}
self.etchLines = {}
for k in range(SampleN*SampleN):
@@ -226,6 +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.
@@ -303,6 +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.
@@ -338,8 +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
@@ -352,6 +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)
@@ -462,14 +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.
@@ -568,6 +660,7 @@ class TZPGcalc():
self.widgets['grating'].value = v['grating']
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()
@@ -658,6 +751,12 @@ class TZPGcalc():
style=style,
layout=layout
)
+ 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')
@@ -668,7 +767,8 @@ class TZPGcalc():
self.widgets['F_y']
]),
HBox([self.widgets['grating'],
- self.widgets['TZPGoffaxis']]),
+ self.widgets['TZPGoffaxis'],
+ self.widgets['3beams']]),
HBox([self.widgets['dr_label_x'],
self.widgets['dr_label_y']]),
HBox([widgets.Label(value='Energy range (eV):'),
@@ -679,6 +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.,
@@ -688,12 +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
)
@@ -702,10 +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,
@@ -724,15 +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,
@@ -742,26 +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
@@ -775,7 +919,7 @@ class TZPGcalc():
layout=layout
)
self.widgets['detX'] = widgets.BoundedFloatText(
- value=20.,
+ value=34.5,
min=-50,
max=50,
step=0.5,
@@ -784,7 +928,7 @@ class TZPGcalc():
layout=layout
)
self.widgets['detY'] = widgets.BoundedFloatText(
- value=0.,
+ value=-2.,
min=-50,
max=50,
step=0.5,
--
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