After ER meeting
This commit is contained in:
rskoupy
@ -2,19 +2,10 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 79,
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"id": "7425242d-3c91-4c1e-a424-08625a38ee7a",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"C:\\Users\\skoupy_r\\Anaconda3\\lib\\site-packages\\scipy\\__init__.py:155: UserWarning: A NumPy version >=1.18.5 and <1.25.0 is required for this version of SciPy (detected version 1.26.1\n",
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" warnings.warn(f\"A NumPy version >={np_minversion} and <{np_maxversion}\"\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"### Initial packages import ###################################################\n",
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"import numpy as np\n",
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@ -25,7 +16,7 @@
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"from pandas import read_excel\n",
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"from IPython.display import display\n",
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"from plotly.subplots import make_subplots\n",
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"from ipywidgets import interactive_output, HBox, VBox, Layout, Label, Valid, ToggleButtons, RadioButtons, Dropdown, IntSlider, Checkbox, Button, ButtonStyle, GridBox\n",
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"from ipywidgets import interactive_output, HBox, VBox, Layout, Label, Valid, ToggleButtons, RadioButtons, Dropdown, IntSlider, Checkbox, Button, ButtonStyle, GridBox,IntSlider\n",
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"\n",
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"# print(\"Numpy version \", np.__version__)\n",
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"# print(\"Pandas version \", pd.__version__)\n",
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@ -300,31 +291,37 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 389,
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"id": "8055b802-cf83-4250-aea9-54e3e6b73db0",
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"metadata": {},
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"outputs": [],
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"source": [
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"### CONTROLS ##########################################\n",
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"\n",
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"ali = dict(style = {'description_width': '60px','button_width': '33px'}, button_style='',disabled=False)\n",
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"ali2 = dict(style = {'description_width': '60px','button_width': '90px'}, button_style='',disabled=False)\n",
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"header = Button(description='STEM control panel',layout=Layout(width='auto', grid_area='header'), style=ButtonStyle(button_color='silver'))\n",
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"ali = dict(style = {'description_width': '60px','button_width': '35px', 'font_weight': 'bold'}, button_style='',disabled = False)\n",
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"ali2 = dict(style = {'description_width': '60px','button_width': '90px', 'font_weight': 'bold'}, button_style='',disabled = False)\n",
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"\n",
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"beam_set = Button(description='Electron beam settings',layout=Layout(width='auto', grid_area='beam_set'), style=ButtonStyle(button_color='lightsteelblue')) \n",
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"\n",
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"\n",
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"\n",
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"\n",
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"\n",
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"header = Button(description='STEM control panel',layout=Layout(width='auto', grid_area='header'), style=ButtonStyle(button_color='silver', font_weight= 'bold',))\n",
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"\n",
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"beam_set = Button(description='Electron beam settings',layout=Layout(width='auto', grid_area='beam_set'), style=ButtonStyle(button_color='lightsteelblue', font_weight= 'bold')) \n",
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"beam = ToggleButtons(options=opt.energies(), value=200,description='E (keV)', layout=Layout(width='auto', grid_area='beam_set1'), **ali)\n",
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"aperture = ToggleButtons(options=opt.apertures(), value='30um', description='Aperture', layout=Layout(width='auto', grid_area='beam_set2'), **ali)\n",
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"probe = ToggleButtons(options=opt.probes(), value='8C', description='Probe', layout=Layout(width='auto', grid_area='beam_set3'), **ali)\n",
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"defocus = IntSlider(description='Δf (nm)', value=0, min=0, max=1000, step=1, continuous_update=False, layout=Layout(width='auto', grid_area='beam_set4'), **ali)\n",
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"\n",
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"scanning_set = Button(description='Scanning parameters',layout=Layout(width='auto', grid_area='scanning_set'),style=ButtonStyle(button_color='lightsteelblue'))\n",
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"scanning_set = Button(description='Scanning parameters',layout=Layout(width='auto', grid_area='scanning_set'),style=ButtonStyle(button_color='lightsteelblue', font_weight= 'bold'))\n",
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"mag = ToggleButtons(options=opt.magnifications(),value=3,description='Mag. Mx', layout=Layout(width='auto', grid_area='scanning_set1'), **ali)\n",
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"matrix = ToggleButtons(options=opt.mappings(), value=2048, description='Matrix', layout=Layout(width='auto', grid_area='scanning_set2'), **ali)\n",
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"dwell_time = ToggleButtons(options=opt.dwelltimes(), value=10, description='t (μs)', layout=Layout(width='auto', grid_area='scanning_set3'), **ali)\n",
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"\n",
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"\n",
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"\n",
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"camera_set = Button(description='Detection',layout=Layout(width='auto', grid_area='camera_set'),style=ButtonStyle(button_color='lightsteelblue'))\n",
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"camera_set = Button(description='Detection',layout=Layout(width='auto', grid_area='camera_set'),style=ButtonStyle(button_color='lightsteelblue', font_weight= 'bold'))\n",
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"cl = ToggleButtons(options=opt.cameralengths(), value=12, description='CL (cm)', layout=Layout(width='auto', grid_area='cl_set1'), **ali)\n",
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"camera = ToggleButtons(options=opt.detectors(), description='Detector', layout=Layout(width='auto', grid_area='camera_set1'), **ali2)\n",
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"restriction = ToggleButtons(options=[('.',False), ('..',True)], value = False, description='PAAR',icons = ['times','check'], layout=Layout(width='auto', grid_area='camera_set2'), **ali)\n",
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@ -348,7 +345,7 @@
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"footer = Button(description='Footer',layout=Layout(width='auto', grid_area='footer'),style=ButtonStyle(button_color='silver'))\n",
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"\n",
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"\n",
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"controls = GridBox(children=[header, beam_set, beam, aperture, probe, defocus, scanning_set, mag,matrix,dwell_time, cl,camera_set, camera, restriction, binning, beam_res, aperture_res,aperture_res2,fov_res, dwell_time_res,footer],\n",
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"controls = GridBox(children=[header, beam_set, beam, aperture, probe, defocus, scanning_set, mag,matrix,dwell_time, cl,camera_set, camera, restriction, binning, beam_res, aperture_res,aperture_res2,fov_res, dwell_time_res],\n",
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" layout=Layout(\n",
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" width='22%',\n",
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" grid_template_rows='auto auto auto',\n",
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@ -375,49 +372,56 @@
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"\n",
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"# SMALL CONTROLS\n",
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"\n",
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"descr = '50px'\n",
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"butt = '30px'\n",
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"descr = '80px'\n",
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"butt = '60px'\n",
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"\n",
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"header = Button(description='Graph controls',layout=Layout(width='auto', grid_area='header'),style=ButtonStyle(button_color='whitesmoke'))\n",
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"header = Button(description='Graph controls',layout=Layout(width='auto', grid_area='header'),style=ButtonStyle(button_color='whitesmoke', font_weight= 'bold'))\n",
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"\n",
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"method = ToggleButtons(options=[('SSB','direct'), ('Iter','iterative')], description='Method', tooltips=['SSB', 'PIE, MLc, DM'],\n",
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" layout=Layout(width='auto', grid_area='methods'), style = {'description_width': descr,'button_width': butt}, button_style='',disabled=False,)\n",
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"method = ToggleButtons(options=[('SSB','direct'), ('Iterative','iterative')], description='Method', tooltips=['SSB', 'PIE, MLc, DM'],\n",
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" layout=Layout(width='auto', grid_area='methods'), style = {'description_width': descr,'button_width': butt, 'font_weight': 'bold'}, button_style='',disabled=False,)\n",
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"\n",
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"graph_size = ToggleButtons(options=[('XXS', 50),('XS', 70),('S', 90), ('M', 100), ('L', 120)], value=100, description='Graphs size',\n",
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"graph_size = IntSlider(value=100,min=10,max=200,step=5, description='Graphs size',\n",
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" layout=Layout(width='auto', grid_area='gr_size'), style = {'description_width': descr,'button_width': butt}, button_style='',disabled=False,)\n",
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"\n",
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"ctf_xaxis = RadioButtons(options=['α','mrad', 'A'], description='CTF x-axis:',\n",
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" layout=Layout(width='auto', grid_area='ctxaxis'), style = {'description_width': descr,'button_width': butt}, disabled=False,)\n",
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"\n",
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"cl_check_laa = Checkbox(value=True, description='Low anlge approximation', indent=False,\n",
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" layout=Layout(width='auto', grid_area='check1'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Low angle approximation check - scattering angle < 10 deg\n",
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"cl_check_pix = Checkbox(value=True, description='Recon. pixel < step size',indent=False,\n",
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" layout=Layout(width='auto', grid_area='check2'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Reconstructed pixel size < scanning step size \n",
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" layout=Layout(width='auto', grid_area='check1'), style = {'description_width': descr}, disabled=False,) # Low angle approximation check - scattering angle < 10 deg\n",
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"cl_check_pix = Checkbox(value=True, description='Ptycho pixel < step size',indent=False,\n",
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" layout=Layout(width='auto', grid_area='check2'), style = {'description_width': descr}, disabled=False,) # Reconstructed pixel size < scanning step size \n",
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"cl_check_def = Checkbox(value=True, description='Beam fits in probe window', indent=False,\n",
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" layout=Layout(width='auto', grid_area='check3'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Is probe window big enough to accomodate defocused probe?\n",
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" layout=Layout(width='auto', grid_area='check3'), style = {'description_width': descr}, disabled=False,) # Is probe window big enough to accomodate defocused probe?\n",
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"cl_check_1bf = Checkbox(value=True, description='Detector cover < 1α', indent=False,\n",
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" layout=Layout(width='auto', grid_area='check4'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Detector cover is lower than 1 α\n",
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" layout=Layout(width='auto', grid_area='check4'), style = {'description_width': descr}, disabled=False,) # Detector cover is lower than 1 α\n",
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"cl_check_nbf = Checkbox(value=True, description='Detector cover > 6α', indent=False,\n",
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" layout=Layout(width='auto', grid_area='check5'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Detector cover is higher than 6 α\n",
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" layout=Layout(width='auto', grid_area='check5'), style = {'description_width': descr}, disabled=False,) # Detector cover is higher than 6 α\n",
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"\n",
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"footer = Button(description='Interactive results',layout=Layout(width='auto', grid_area='footer'),style=ButtonStyle(button_color='whitesmoke'))\n",
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"\n",
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"small_controls = GridBox(children=[header, method, graph_size, ctf_xaxis, cl_check_laa,cl_check_pix,cl_check_def, cl_check_1bf, cl_check_nbf, footer],\n",
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"chart = ToggleButtons(options=[('STEM','micr'), ('Charts','dedic'),('Both','both')],value = 'both', description='Show',\n",
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" layout=Layout(width='auto', grid_area='charts'), style = {'description_width': descr,'button_width': butt, 'font_weight': 'bold'}, button_style='',disabled=False,)\n",
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"\n",
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"\n",
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"footer = Button(description='Interactive results',layout=Layout(width='auto', grid_area='footer'),style=ButtonStyle(button_color='whitesmoke', font_weight= 'bold'))\n",
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"\n",
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"small_controls = GridBox(children=[header, method, chart, graph_size, ctf_xaxis, cl_check_laa,cl_check_pix,cl_check_def, cl_check_1bf, cl_check_nbf, footer],\n",
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" layout=Layout(\n",
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" width='100%',\n",
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" grid_template_rows='auto auto auto',\n",
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" grid_template_columns='40% 20% 20% 20%',\n",
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" grid_template_columns='50% 20% 30%',\n",
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" grid_template_areas='''\n",
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" \"header header header header \"\n",
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" \"methods ctxaxis check1 check2\"\n",
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" \"gr_size ctxaxis check3 check5\"\n",
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" \". ctxaxis check4 . \" \n",
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" \"footer footer footer footer\"\n",
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" \"header header header \"\n",
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" \"methods ctxaxis check1 \"\n",
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" \"charts ctxaxis check2 \"\n",
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" \"gr_size ctxaxis check3 \"\n",
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" \". . check4 \"\n",
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" \". . check5 \"\n",
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" \"footer footer footer\"\n",
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" ''')\n",
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" )\n",
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"\n",
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"\n",
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"def ptycho_interact(beam, aperture, aperture_res, aperture_res2, probe, cl, matrix, defocus, mag, camera, binning, dwell_time, restriction, method, ctf_xaxis, cl_check_laa, cl_check_pix, cl_check_def, cl_check_1bf, cl_check_nbf, graph_size):\n",
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"def ptycho_interact(beam, aperture, aperture_res, aperture_res2, probe, cl, matrix, defocus, mag, camera, binning, dwell_time, restriction, method, ctf_xaxis, cl_check_laa, cl_check_pix, cl_check_def, cl_check_1bf, cl_check_nbf, graph_size, chart):\n",
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" \n",
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" ### SINGLE SETTING PARAMETERS ###\n",
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" wavelength = pty.get_wavelength(beam)*1e12\n",
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@ -464,59 +468,90 @@
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" pctf = pty.get_ssb_ctf()\n",
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" apertury = opt.apertures()\n",
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" \n",
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"\n",
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"\n",
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"\n",
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"\n",
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"\n",
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" \n",
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" ### SAMPLE PLANE ##########################################\n",
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" points = 5\n",
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" yyy = np.append(np.linspace(0,overlap,100), 200)\n",
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" wid = np.linspace(0,points-1,points) * step_size_corr\n",
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" wid = np.array([-2, -1, 0, 1, 2]) * step_size_corr\n",
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" \n",
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" fig5 = make_subplots(specs=[[{\"secondary_y\": True}]])\n",
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" fig5.update_xaxes(title_text=\"Sample plane (nm)\", range=[0, points*step_size_corr], showgrid=False, zeroline=False)\n",
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" fig5.update_yaxes(range=[0, points*step_size_corr],showgrid=False, showticklabels=False)\n",
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" fig5.update_xaxes(title_text=\"Sample plane (nm)\", range=[-4*step_size_corr, 4*step_size_corr], showgrid=False, zeroline=False)\n",
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" fig5.update_yaxes(range=[-4*step_size_corr, 4*step_size_corr],showgrid=False, showticklabels=False)\n",
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" for x in range(len(wid)):\n",
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" fig5.add_trace(go.Scatter(showlegend=False, x=wid, y=np.ones(len(wid))*wid[x], marker_color='blue'),secondary_y=False)\n",
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" for x in range(len(wid)): \n",
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" for y in range(len(wid)): \n",
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" fig5.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", opacity=0.1, fillcolor=\"#FF7F7F\",name=False, x0=wid[x]-beam_diameter/2, y0=wid[y]-beam_diameter/2, x1=wid[x]+beam_diameter/2, y1=wid[y]+beam_diameter/2, line_color=\"red\",secondary_y=False)\n",
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"\n",
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" fig5.add_trace(go.Scatter(showlegend=True, x=[-1], y=[-1],marker_size=12, marker_color='blue', name='Step '+str(np.round(10*step_size,3))+' Å ('+str(np.round(10*step_size_corr,3))+')'))\n",
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" fig5.add_annotation(x=-1*step_size_corr, y=-2*step_size_corr, ax=-2*step_size_corr, ay=-2*step_size_corr, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
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" fig5.add_annotation(x=-2*step_size_corr, y=-1*step_size_corr, ax=-2*step_size_corr, ay=-2*step_size_corr, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
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" fig5.add_annotation(x=-1.25*step_size_corr, y=-1.5*step_size_corr, text=str(np.round(10*step_size_corr,3))+' Å', showarrow=False, yshift=0)\n",
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" \n",
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" fig5.add_annotation(x=2*step_size_corr-0.75*beam_diameter/2, y=-2*step_size_corr-0.75*beam_diameter/2, ax=2*step_size_corr, ay=-2*step_size_corr,xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
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" fig5.add_annotation(x=2*step_size_corr+0.75*beam_diameter/2, y=-2*step_size_corr+0.75*beam_diameter/2, ax=2*step_size_corr, ay=-2*step_size_corr,xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
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" fig5.add_annotation(x=2.25*step_size_corr, y=-2*step_size_corr, text=str(np.round(10*beam_diameter,2))+' Å', showarrow=False, yshift=-15)\n",
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" \n",
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" \n",
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" if method == 'direct':\n",
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" xx = 2*wavelength/(np.sin(semi_angle_corr*omega/1000))/100\n",
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" fig5.add_trace(go.Scatter(showlegend=True, x=[-1], y=[-1],marker_size=12, marker_color='green', name='Rec step '+str(np.round(xx[-1]/3,2))+' Å')) \n",
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" \n",
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" fig5.add_trace(go.Scatter(showlegend=True, x=[-1], y=[-1],marker_size=12, marker_color='#FF7F7F', name='Beam ⌀ '+ str(np.round(10*beam_diameter,2))+\" Å\"))\n",
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" fig5.update_layout(legend=dict(orientation=\"v\",yanchor=\"bottom\",y=0.85,xanchor=\"right\",x=0.9))\n",
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" fig5.add_trace(go.Scatter(showlegend=False, x = points*step_size_corr*np.ones(len(yyy)), y=yyy, opacity=1,mode='markers',marker_symbol = \"triangle-down\",marker=dict(size=20, color=yyy, colorscale='rainbow_r', showscale=False)),secondary_y=True) \n",
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" fig5.update_yaxes(title_text=\"Overlap %\", range=[0, 100],showgrid=False, showticklabels=True, tickvals = [0, 20, 40,50, 60,70, 80, 90, 100], secondary_y=True)\n",
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" fig5.update_layout(title={'text': \"Sample\",'y':0.95, 'x':0.30,'xanchor': 'left','yanchor': 'top'})\n",
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" fig5.add_trace(go.Scatter(showlegend=False, x = -4*step_size_corr*np.ones(len(yyy)), y=yyy, opacity=1,mode='markers',marker_symbol = \"triangle-down\",marker=dict(size=20, color=yyy, colorscale='rainbow_r', showscale=False)),secondary_y=True) \n",
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" fig5.update_yaxes(range=[0, 100], showgrid=False, showticklabels=False, secondary_y=True)\n",
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" fig5.update_yaxes(title_text=\"Overlap %\", showgrid=False, showticklabels=True, tickvals = [-4*step_size_corr, -2*step_size_corr, 0, 2*step_size_corr, 4*step_size_corr],ticktext = ['0', '25', '50', '75', '100'], secondary_y=False)\n",
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" fig5.update_layout(title={'text': \"Sample\",'y': 0.975, 'x': 0.30,'xanchor': 'left','yanchor': 'top'})\n",
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" fig5.update_layout(width=4.5*graph_size, height=3.0*graph_size, margin =dict(l=1.3*graph_size, r=0.3*graph_size, t=0.1*graph_size, b=0))\n",
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"\n",
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" \n",
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"\n",
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" \n",
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" \n",
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" \n",
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" \n",
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" \n",
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" \n",
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" \n",
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" ### DETECTOR PLANE ##########################################\n",
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" fig6 = go.Figure() \n",
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" fig6.update_xaxes(title_text=\"Pixels\", range=[1, num_pixels], zeroline=False)\n",
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" fig6.update_yaxes(range=[1, num_pixels], showticklabels=False,)\n",
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" for x in np.linspace(1,int(np.round(covered_alfas)),int(np.round(covered_alfas))):\n",
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" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", x0=num_pixels/2-x*beam_diameter_pix, y0=num_pixels/2-x*beam_diameter_pix, x1=num_pixels/2+x*beam_diameter_pix, y1=num_pixels/2+x*beam_diameter_pix,line_color=\"gray\")\n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=False,x=[num_pixels/2],y=[num_pixels/2-x*beam_diameter_pix],mode=\"lines+text\", text=str(int(2*x))+\"α\",textposition=\"top center\"))\n",
|
||||
" fig6 = make_subplots(specs=[[{\"secondary_y\": True}]])\n",
|
||||
" \n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", fillcolor=\"#FF7F7F\", x0=num_pixels/2-beam_diameter_pix/2, y0=num_pixels/2-beam_diameter_pix/2, x1=num_pixels/2+beam_diameter_pix/2, y1=num_pixels/2+beam_diameter_pix/2,line_color=\"#FF7F7F\")\n",
|
||||
" fig6.add_annotation(x=num_pixels/2-beam_diameter_pix/2, y=num_pixels/2, ax=num_pixels/2+beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=3,arrowsize=1,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig6.add_annotation(x=num_pixels/2+beam_diameter_pix/2,y=num_pixels/2, ax=num_pixels/2-beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y', text='', showarrow=True,arrowhead=3,arrowsize=1,arrowwidth=1,arrowcolor='black')\n",
|
||||
" for x in np.linspace(1,int(np.round(covered_alfas)),int(np.round(covered_alfas))):\n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", x0=num_pixels/2-x*beam_diameter_pix, y0=num_pixels/2-x*beam_diameter_pix, x1=num_pixels/2+x*beam_diameter_pix, y1=num_pixels/2+x*beam_diameter_pix, line=dict(color=\"gray\",width=1,dash=\"dot\",),secondary_y=False)\n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=False,x=[num_pixels/2],y=[num_pixels/2+x*beam_diameter_pix],mode=\"lines+text\", text=str(int(2*x))+\"α\",textposition=\"top center\"),secondary_y=False)\n",
|
||||
" \n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\",opacity=0.5, fillcolor=\"#FF7F7F\", x0=num_pixels/2-beam_diameter_pix/2, y0=num_pixels/2-beam_diameter_pix/2, x1=num_pixels/2+beam_diameter_pix/2, y1=num_pixels/2+beam_diameter_pix/2,line_color=\"#FF7F7F\",secondary_y=False)\n",
|
||||
" fig6.add_annotation(x=num_pixels/2-beam_diameter_pix/2, y=num_pixels/2, ax=num_pixels/2+beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig6.add_annotation(x=num_pixels/2+beam_diameter_pix/2,y=num_pixels/2, ax=num_pixels/2-beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y', text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig6.add_annotation(x=num_pixels/2, y=num_pixels/2, text=str(np.round(beam_diameter_pix,1))+\" pix\", showarrow=False, yshift=10)\n",
|
||||
" fig6.add_trace(go.Scatter(x=[1,1.5,1,1.5], y=[1,1,1.5,1.5], name='Pix ∠ ' +str(np.round(pixel_angle,2))+' mrad'))\n",
|
||||
" fig6.add_trace(go.Scatter(x=[1,1.5,1,1.5], y=[1,1,1.5,1.5], name='Pixel size ' +str(np.round(size_pixel,2))+' um'))\n",
|
||||
" fig6.update_layout(legend=dict(orientation=\"v\",yanchor=\"bottom\",y=0.80,xanchor=\"right\",x=1))\n",
|
||||
" fig6.update_layout(title={'text': \"Detector\",'y':0.95, 'x':0.11,'xanchor': 'left','yanchor': 'top'})\n",
|
||||
" fig6.update_layout(xaxis = dict(tickmode = 'array', tickvals = [1, num_pixels/4, num_pixels/2, 3*num_pixels/4, num_pixels])) \n",
|
||||
" fig6.update_layout(width=3.5*graph_size, height=3*graph_size, margin = dict(l=0.35*graph_size, r=0.65*graph_size, t=0.3*graph_size, b=0))\n",
|
||||
" fig6.add_annotation(x=num_pixels/2, y=num_pixels/2, text=\"1 pix = \"+str(np.round(pixel_angle,2))+\" mrad\", showarrow=False, yshift=-10)\n",
|
||||
" fig6.add_annotation(x=num_pixels/2, y=num_pixels/10, text=\"Real pixel size = \"+str(np.round(size_pixel,2))+\" μm\", showarrow=False, yshift=0)\n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=True,x=[-1], y=[-1], marker_color='red', name = \"BF disk\"),secondary_y=False)\n",
|
||||
" \n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=False,x=[-1], y=[-1]),secondary_y=True)\n",
|
||||
" \n",
|
||||
" fig6.update_layout(legend=dict(orientation=\"h\",yanchor=\"bottom\",y=1.00,xanchor=\"right\",x=0.9))\n",
|
||||
" fig6.update_layout(title={'text': \"Detector\",'y':0.975, 'x':0.11,'xanchor': 'left','yanchor': 'top'})\n",
|
||||
" \n",
|
||||
" fig6.update_xaxes(title_text=\"Pixels\", range=[1, num_pixels], zeroline=False, tickvals = [1, num_pixels/4, num_pixels/2, 3*num_pixels/4, num_pixels]) \n",
|
||||
" fig6.update_yaxes(range=[1, num_pixels], showticklabels=False, showgrid=False, secondary_y=False)\n",
|
||||
" fig6.update_yaxes(title_text=\"Angular cover (mrad)\", range=[1, num_pixels], showticklabels=True, tickvals = [1, num_pixels/4, num_pixels/2, 3*num_pixels/4, num_pixels], ticktext = ['', np.round(detector_cover/4,1), np.round(detector_cover/2,1), np.round(3*detector_cover/4,1), np.round(detector_cover,1)], secondary_y=True) \n",
|
||||
" \n",
|
||||
" fig6.update_layout(width=3.5*graph_size, height=3*graph_size, margin = dict(l=0.35*graph_size, r=0.48*graph_size, t=0.3*graph_size, b=0))\n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" focusdepth = wavelength/(semi_angle_corr/1000)**2/1000\n",
|
||||
" ssb_cl, kolik = pty.cl4ssb(detector_cover_a_all)\n",
|
||||
" ### MICROSCOPE SCHEME ##########################################\n",
|
||||
@ -654,20 +689,27 @@
|
||||
" fig4.update_layout(xaxis = dict(tickmode = 'array', tickvals = opt.cameralengths()))\n",
|
||||
" fig4.update_layout(width=8.0*graph_size, height=2.25*graph_size, margin =dict(l=1.3*graph_size, r=0.25*graph_size, t=0.3*graph_size, b=0.3*graph_size))\n",
|
||||
"\n",
|
||||
" ### SHOWING ###\n",
|
||||
" right_column = VBox([go.FigureWidget(fig),HBox([go.FigureWidget(fig5),go.FigureWidget(fig6)]),go.FigureWidget(fig4)])\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" \n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" ### SHOWING ###\n",
|
||||
" if chart == 'micr':\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" total = HBox([left_column]) \n",
|
||||
" \n",
|
||||
" total = HBox([left_column, right_column])\n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px')\n",
|
||||
" \n",
|
||||
" elif chart == 'dedic':\n",
|
||||
" right_column = VBox([go.FigureWidget(fig) ,HBox([go.FigureWidget(fig5),go.FigureWidget(fig6)]),go.FigureWidget(fig4)])\n",
|
||||
" total = HBox([right_column])\n",
|
||||
" \n",
|
||||
" else: \n",
|
||||
" right_column = VBox([go.FigureWidget(fig) ,HBox([go.FigureWidget(fig5),go.FigureWidget(fig6)]),go.FigureWidget(fig4)])\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" total = HBox([left_column, right_column])\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px') \n",
|
||||
" display(total)\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" if method == 'iterative': \n",
|
||||
@ -781,7 +823,7 @@
|
||||
" \n",
|
||||
" dictionary[i] = ToggleButtons(options=data_tuple, button_style=button_style, icons = icons, **align6)\n",
|
||||
" \n",
|
||||
" legend = ToggleButtons(options=['Ptycho pix. (Å)','Det. cover (mrad)','Det. cover (α)', 'Max. def. (nm)','Selected by CL ','Nominal CL (cm)',], \n",
|
||||
" legend = ToggleButtons(options=['Ptycho pixel (Å)','Det. cover (mrad)','Det. cover (α)', 'Max. def. (nm)','Selected by CL ','Nominal CL (cm)',], \n",
|
||||
" tooltips=['Dependent on: detector, beam energy, camera length',\n",
|
||||
" 'Dependent on: detector, camera length',\n",
|
||||
" 'Dependent on: detector, camera length, probe semi-angle',\n",
|
||||
@ -796,22 +838,32 @@
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" ### SHOWING ###\n",
|
||||
" sample_overlap = HBox([go.FigureWidget(fig5), go.FigureWidget(fig7), go.FigureWidget(fig6)]) \n",
|
||||
" right_column = VBox([HBox([go.FigureWidget(fig),checks]), sample_overlap, cltab]) \n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)]) \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" total = HBox([left_column, right_column])\n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px')\n",
|
||||
" \n",
|
||||
" if chart == 'micr':\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" total = HBox([left_column]) \n",
|
||||
" \n",
|
||||
" elif chart == 'dedic':\n",
|
||||
" sample_overlap = HBox([go.FigureWidget(fig5), go.FigureWidget(fig7), go.FigureWidget(fig6)]) \n",
|
||||
" right_column = VBox([HBox([go.FigureWidget(fig),checks]), sample_overlap, cltab]) \n",
|
||||
" total = HBox([right_column])\n",
|
||||
" \n",
|
||||
" else: \n",
|
||||
" sample_overlap = HBox([go.FigureWidget(fig5), go.FigureWidget(fig7), go.FigureWidget(fig6)]) \n",
|
||||
" right_column = VBox([HBox([go.FigureWidget(fig),checks]), sample_overlap, cltab]) \n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)]) \n",
|
||||
" total = HBox([left_column, right_column]) \n",
|
||||
" \n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px') \n",
|
||||
" display(total)\n",
|
||||
"\n",
|
||||
" \n",
|
||||
" return \n",
|
||||
" \n",
|
||||
"gui = interactive_output(ptycho_interact, {\"beam\": beam, \"aperture\": aperture,\"aperture_res\": aperture_res,\"aperture_res2\": aperture_res2, \"probe\": probe, \"cl\": cl, \"matrix\": matrix, \"defocus\": defocus, \"mag\": mag, \"camera\": camera,\n",
|
||||
" \"binning\": binning, \"dwell_time\": dwell_time, \"restriction\": restriction, \"method\": method, \"ctf_xaxis\": ctf_xaxis,\n",
|
||||
" \"cl_check_laa\":cl_check_laa, \"cl_check_pix\": cl_check_pix, \"cl_check_def\": cl_check_def, \"cl_check_1bf\": cl_check_1bf, \"cl_check_nbf\": cl_check_nbf, \"graph_size\": graph_size}) \n",
|
||||
" \"cl_check_laa\":cl_check_laa, \"cl_check_pix\": cl_check_pix, \"cl_check_def\": cl_check_def, \"cl_check_1bf\": cl_check_1bf, \"cl_check_nbf\": cl_check_nbf, \"graph_size\": graph_size,\"chart\": chart}) \n",
|
||||
"\n"
|
||||
]
|
||||
},
|
||||
@ -845,14 +897,14 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"execution_count": 390,
|
||||
"id": "7937f054-fcd0-4e67-a20f-7696f5903a94",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"application/vnd.jupyter.widget-view+json": {
|
||||
"model_id": "47642ef0d8b94bceb11f878293997c33",
|
||||
"model_id": "6f84c5e6c29142a9bb9db08cd48aefbd",
|
||||
"version_major": 2,
|
||||
"version_minor": 0
|
||||
},
|
||||
@ -865,6 +917,7 @@
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"\n",
|
||||
"display(HBox([controls, VBox([small_controls, gui]) ]))"
|
||||
]
|
||||
},
|
||||
@ -888,6 +941,139 @@
|
||||
"# import ipywidgets\n",
|
||||
"# print(\"Ipywidgets version \", ipywidgets.__version__)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "33727cb4-c3d7-4134-be89-f10b9922fbda",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 75,
|
||||
"id": "1cb358ba-42c4-420a-a0a6-0de425e670a6",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"Ipywidgets version 7.6.5\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"import ipywidgets\n",
|
||||
"print(\"Ipywidgets version \", ipywidgets.__version__)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "a52ff861-8243-4d39-b7da-1ee8fb0ee494",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "61970cec-8678-4edf-99f6-4f832d2aad8d",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"https://ipywidgets.readthedocs.io/en/latest/user_install.html"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 386,
|
||||
"id": "a4628def-4c43-456e-a93b-95952e2a3dea",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<ul>\n",
|
||||
"<li><b>DescriptionStyle:</b> BoundedFloatText, BoundedIntText, Checkbox, ColorPicker, Combobox, DatePicker, Dropdown, FloatText, HTML, HTMLMath, IntText, Label, Password, Play, RadioButtons, Select, SelectMultiple, SelectionRangeSlider, SelectionSlider, Text, Textarea, ToggleButton, Valid</li>\n",
|
||||
"<li><b>ButtonStyle:</b> Button, FileUpload</li>\n",
|
||||
"<li><b>SliderStyle:</b> FloatLogSlider, FloatRangeSlider, FloatSlider, IntRangeSlider, IntSlider</li>\n",
|
||||
"<li><b>ProgressStyle:</b> FloatProgress, IntProgress</li>\n",
|
||||
"<li><b>ToggleButtonsStyle:</b> ToggleButtons</li></ul>"
|
||||
],
|
||||
"text/plain": [
|
||||
"<IPython.core.display.HTML object>"
|
||||
]
|
||||
},
|
||||
"execution_count": 386,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"from collections import defaultdict\n",
|
||||
"from IPython.display import HTML\n",
|
||||
"import ipywidgets\n",
|
||||
"from pprint import pprint\n",
|
||||
"\n",
|
||||
"reverse_lut = defaultdict(set)\n",
|
||||
"styles = set()\n",
|
||||
"for export_name in dir(ipywidgets.widgets):\n",
|
||||
" export = getattr(ipywidgets.widgets, export_name)\n",
|
||||
" try:\n",
|
||||
" if issubclass(export, ipywidgets.Widget) and 'style' in export.class_trait_names():\n",
|
||||
" reverse_lut[export.style.klass.__name__].add(export.__name__)\n",
|
||||
" styles.add(export.style.klass)\n",
|
||||
" except TypeError:\n",
|
||||
" pass\n",
|
||||
"\n",
|
||||
"html = '<ul>'\n",
|
||||
"for style, widgets in reverse_lut.items():\n",
|
||||
" html = f\"{html}\\n<li><b>{style}:</b> {', '.join(sorted(widgets))}</li>\"\n",
|
||||
"html += \"</ul>\"\n",
|
||||
"HTML(html)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 74,
|
||||
"id": "54c1add7-f5ec-43f0-a447-e22dd03926a7",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<table>\n",
|
||||
"<tr><th>Attribute</th><th>ToggleButtonsStyle</th><th>ButtonStyle</th><th>DescriptionStyle</th><th>ProgressStyle</th><th>SliderStyle</th></tr><tr><td>description_width</td><td>✓</td><td></td><td>✓</td><td>✓</td><td>✓</td></tr><tr><td>button_width</td><td>✓</td><td></td><td></td><td></td><td></td></tr><tr><td>font_weight</td><td>✓</td><td>✓</td><td></td><td></td><td></td></tr><tr><td>bar_color</td><td></td><td></td><td></td><td>✓</td><td></td></tr><tr><td>handle_color</td><td></td><td></td><td></td><td></td><td>✓</td></tr><tr><td>button_color</td><td></td><td>✓</td><td></td><td></td><td></td></tr></table>"
|
||||
],
|
||||
"text/plain": [
|
||||
"<IPython.core.display.HTML object>"
|
||||
]
|
||||
},
|
||||
"execution_count": 74,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"attributes = defaultdict(set)\n",
|
||||
"base_traits = set(ipywidgets.Style.class_trait_names())\n",
|
||||
"\n",
|
||||
"for s in styles:\n",
|
||||
" for t in s.class_trait_names():\n",
|
||||
" if not t.startswith(\"_\") and t not in base_traits:\n",
|
||||
" attributes[s.__name__].add(t)\n",
|
||||
"all_attributes = set().union(*attributes.values())\n",
|
||||
"\n",
|
||||
"html = '<table>\\n'\n",
|
||||
"html = f\"{html}<tr><th>Attribute</th>{ ''.join(f'<th>{s}</th>' for s in attributes.keys()) }</tr>\"\n",
|
||||
"for a in all_attributes:\n",
|
||||
" html = f\"\"\"{html}<tr><td>{a}</td>{ ''.join(f'<td>{\"✓\" if a in attribs else \"\"}</td>' for attribs in attributes.values()) }</tr>\"\"\"\n",
|
||||
"html += \"</table>\"\n",
|
||||
"HTML(html)"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
|
||||
Binary file not shown.
@ -2,19 +2,10 @@
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 1,
|
||||
"execution_count": 79,
|
||||
"id": "7425242d-3c91-4c1e-a424-08625a38ee7a",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stderr",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"C:\\Users\\skoupy_r\\Anaconda3\\lib\\site-packages\\scipy\\__init__.py:155: UserWarning: A NumPy version >=1.18.5 and <1.25.0 is required for this version of SciPy (detected version 1.26.1\n",
|
||||
" warnings.warn(f\"A NumPy version >={np_minversion} and <{np_maxversion}\"\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"### Initial packages import ###################################################\n",
|
||||
"import numpy as np\n",
|
||||
@ -25,7 +16,7 @@
|
||||
"from pandas import read_excel\n",
|
||||
"from IPython.display import display\n",
|
||||
"from plotly.subplots import make_subplots\n",
|
||||
"from ipywidgets import interactive_output, HBox, VBox, Layout, Label, Valid, ToggleButtons, RadioButtons, Dropdown, IntSlider, Checkbox, Button, ButtonStyle, GridBox\n",
|
||||
"from ipywidgets import interactive_output, HBox, VBox, Layout, Label, Valid, ToggleButtons, RadioButtons, Dropdown, IntSlider, Checkbox, Button, ButtonStyle, GridBox,IntSlider\n",
|
||||
"\n",
|
||||
"# print(\"Numpy version \", np.__version__)\n",
|
||||
"# print(\"Pandas version \", pd.__version__)\n",
|
||||
@ -300,31 +291,37 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 4,
|
||||
"execution_count": 389,
|
||||
"id": "8055b802-cf83-4250-aea9-54e3e6b73db0",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"### CONTROLS ##########################################\n",
|
||||
"\n",
|
||||
"ali = dict(style = {'description_width': '60px','button_width': '33px'}, button_style='',disabled=False)\n",
|
||||
"ali2 = dict(style = {'description_width': '60px','button_width': '90px'}, button_style='',disabled=False)\n",
|
||||
"header = Button(description='STEM control panel',layout=Layout(width='auto', grid_area='header'), style=ButtonStyle(button_color='silver'))\n",
|
||||
"ali = dict(style = {'description_width': '60px','button_width': '35px', 'font_weight': 'bold'}, button_style='',disabled = False)\n",
|
||||
"ali2 = dict(style = {'description_width': '60px','button_width': '90px', 'font_weight': 'bold'}, button_style='',disabled = False)\n",
|
||||
"\n",
|
||||
"beam_set = Button(description='Electron beam settings',layout=Layout(width='auto', grid_area='beam_set'), style=ButtonStyle(button_color='lightsteelblue')) \n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"header = Button(description='STEM control panel',layout=Layout(width='auto', grid_area='header'), style=ButtonStyle(button_color='silver', font_weight= 'bold',))\n",
|
||||
"\n",
|
||||
"beam_set = Button(description='Electron beam settings',layout=Layout(width='auto', grid_area='beam_set'), style=ButtonStyle(button_color='lightsteelblue', font_weight= 'bold')) \n",
|
||||
"beam = ToggleButtons(options=opt.energies(), value=200,description='E (keV)', layout=Layout(width='auto', grid_area='beam_set1'), **ali)\n",
|
||||
"aperture = ToggleButtons(options=opt.apertures(), value='30um', description='Aperture', layout=Layout(width='auto', grid_area='beam_set2'), **ali)\n",
|
||||
"probe = ToggleButtons(options=opt.probes(), value='8C', description='Probe', layout=Layout(width='auto', grid_area='beam_set3'), **ali)\n",
|
||||
"defocus = IntSlider(description='Δf (nm)', value=0, min=0, max=1000, step=1, continuous_update=False, layout=Layout(width='auto', grid_area='beam_set4'), **ali)\n",
|
||||
"\n",
|
||||
"scanning_set = Button(description='Scanning parameters',layout=Layout(width='auto', grid_area='scanning_set'),style=ButtonStyle(button_color='lightsteelblue'))\n",
|
||||
"scanning_set = Button(description='Scanning parameters',layout=Layout(width='auto', grid_area='scanning_set'),style=ButtonStyle(button_color='lightsteelblue', font_weight= 'bold'))\n",
|
||||
"mag = ToggleButtons(options=opt.magnifications(),value=3,description='Mag. Mx', layout=Layout(width='auto', grid_area='scanning_set1'), **ali)\n",
|
||||
"matrix = ToggleButtons(options=opt.mappings(), value=2048, description='Matrix', layout=Layout(width='auto', grid_area='scanning_set2'), **ali)\n",
|
||||
"dwell_time = ToggleButtons(options=opt.dwelltimes(), value=10, description='t (μs)', layout=Layout(width='auto', grid_area='scanning_set3'), **ali)\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"camera_set = Button(description='Detection',layout=Layout(width='auto', grid_area='camera_set'),style=ButtonStyle(button_color='lightsteelblue'))\n",
|
||||
"camera_set = Button(description='Detection',layout=Layout(width='auto', grid_area='camera_set'),style=ButtonStyle(button_color='lightsteelblue', font_weight= 'bold'))\n",
|
||||
"cl = ToggleButtons(options=opt.cameralengths(), value=12, description='CL (cm)', layout=Layout(width='auto', grid_area='cl_set1'), **ali)\n",
|
||||
"camera = ToggleButtons(options=opt.detectors(), description='Detector', layout=Layout(width='auto', grid_area='camera_set1'), **ali2)\n",
|
||||
"restriction = ToggleButtons(options=[('.',False), ('..',True)], value = False, description='PAAR',icons = ['times','check'], layout=Layout(width='auto', grid_area='camera_set2'), **ali)\n",
|
||||
@ -348,7 +345,7 @@
|
||||
"footer = Button(description='Footer',layout=Layout(width='auto', grid_area='footer'),style=ButtonStyle(button_color='silver'))\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"controls = GridBox(children=[header, beam_set, beam, aperture, probe, defocus, scanning_set, mag,matrix,dwell_time, cl,camera_set, camera, restriction, binning, beam_res, aperture_res,aperture_res2,fov_res, dwell_time_res,footer],\n",
|
||||
"controls = GridBox(children=[header, beam_set, beam, aperture, probe, defocus, scanning_set, mag,matrix,dwell_time, cl,camera_set, camera, restriction, binning, beam_res, aperture_res,aperture_res2,fov_res, dwell_time_res],\n",
|
||||
" layout=Layout(\n",
|
||||
" width='22%',\n",
|
||||
" grid_template_rows='auto auto auto',\n",
|
||||
@ -375,49 +372,56 @@
|
||||
"\n",
|
||||
"# SMALL CONTROLS\n",
|
||||
"\n",
|
||||
"descr = '50px'\n",
|
||||
"butt = '30px'\n",
|
||||
"descr = '80px'\n",
|
||||
"butt = '60px'\n",
|
||||
"\n",
|
||||
"header = Button(description='Graph controls',layout=Layout(width='auto', grid_area='header'),style=ButtonStyle(button_color='whitesmoke'))\n",
|
||||
"header = Button(description='Graph controls',layout=Layout(width='auto', grid_area='header'),style=ButtonStyle(button_color='whitesmoke', font_weight= 'bold'))\n",
|
||||
"\n",
|
||||
"method = ToggleButtons(options=[('SSB','direct'), ('Iter','iterative')], description='Method', tooltips=['SSB', 'PIE, MLc, DM'],\n",
|
||||
" layout=Layout(width='auto', grid_area='methods'), style = {'description_width': descr,'button_width': butt}, button_style='',disabled=False,)\n",
|
||||
"method = ToggleButtons(options=[('SSB','direct'), ('Iterative','iterative')], description='Method', tooltips=['SSB', 'PIE, MLc, DM'],\n",
|
||||
" layout=Layout(width='auto', grid_area='methods'), style = {'description_width': descr,'button_width': butt, 'font_weight': 'bold'}, button_style='',disabled=False,)\n",
|
||||
"\n",
|
||||
"graph_size = ToggleButtons(options=[('XXS', 50),('XS', 70),('S', 90), ('M', 100), ('L', 120)], value=100, description='Graphs size',\n",
|
||||
"graph_size = IntSlider(value=100,min=10,max=200,step=5, description='Graphs size',\n",
|
||||
" layout=Layout(width='auto', grid_area='gr_size'), style = {'description_width': descr,'button_width': butt}, button_style='',disabled=False,)\n",
|
||||
"\n",
|
||||
"ctf_xaxis = RadioButtons(options=['α','mrad', 'A'], description='CTF x-axis:',\n",
|
||||
" layout=Layout(width='auto', grid_area='ctxaxis'), style = {'description_width': descr,'button_width': butt}, disabled=False,)\n",
|
||||
"\n",
|
||||
"cl_check_laa = Checkbox(value=True, description='Low anlge approximation', indent=False,\n",
|
||||
" layout=Layout(width='auto', grid_area='check1'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Low angle approximation check - scattering angle < 10 deg\n",
|
||||
"cl_check_pix = Checkbox(value=True, description='Recon. pixel < step size',indent=False,\n",
|
||||
" layout=Layout(width='auto', grid_area='check2'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Reconstructed pixel size < scanning step size \n",
|
||||
" layout=Layout(width='auto', grid_area='check1'), style = {'description_width': descr}, disabled=False,) # Low angle approximation check - scattering angle < 10 deg\n",
|
||||
"cl_check_pix = Checkbox(value=True, description='Ptycho pixel < step size',indent=False,\n",
|
||||
" layout=Layout(width='auto', grid_area='check2'), style = {'description_width': descr}, disabled=False,) # Reconstructed pixel size < scanning step size \n",
|
||||
"cl_check_def = Checkbox(value=True, description='Beam fits in probe window', indent=False,\n",
|
||||
" layout=Layout(width='auto', grid_area='check3'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Is probe window big enough to accomodate defocused probe?\n",
|
||||
" layout=Layout(width='auto', grid_area='check3'), style = {'description_width': descr}, disabled=False,) # Is probe window big enough to accomodate defocused probe?\n",
|
||||
"cl_check_1bf = Checkbox(value=True, description='Detector cover < 1α', indent=False,\n",
|
||||
" layout=Layout(width='auto', grid_area='check4'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Detector cover is lower than 1 α\n",
|
||||
" layout=Layout(width='auto', grid_area='check4'), style = {'description_width': descr}, disabled=False,) # Detector cover is lower than 1 α\n",
|
||||
"cl_check_nbf = Checkbox(value=True, description='Detector cover > 6α', indent=False,\n",
|
||||
" layout=Layout(width='auto', grid_area='check5'), style = {'description_width': descr,'button_width': butt}, disabled=False,) # Detector cover is higher than 6 α\n",
|
||||
" layout=Layout(width='auto', grid_area='check5'), style = {'description_width': descr}, disabled=False,) # Detector cover is higher than 6 α\n",
|
||||
"\n",
|
||||
"footer = Button(description='Interactive results',layout=Layout(width='auto', grid_area='footer'),style=ButtonStyle(button_color='whitesmoke'))\n",
|
||||
"\n",
|
||||
"small_controls = GridBox(children=[header, method, graph_size, ctf_xaxis, cl_check_laa,cl_check_pix,cl_check_def, cl_check_1bf, cl_check_nbf, footer],\n",
|
||||
"chart = ToggleButtons(options=[('STEM','micr'), ('Charts','dedic'),('Both','both')],value = 'both', description='Show',\n",
|
||||
" layout=Layout(width='auto', grid_area='charts'), style = {'description_width': descr,'button_width': butt, 'font_weight': 'bold'}, button_style='',disabled=False,)\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"footer = Button(description='Interactive results',layout=Layout(width='auto', grid_area='footer'),style=ButtonStyle(button_color='whitesmoke', font_weight= 'bold'))\n",
|
||||
"\n",
|
||||
"small_controls = GridBox(children=[header, method, chart, graph_size, ctf_xaxis, cl_check_laa,cl_check_pix,cl_check_def, cl_check_1bf, cl_check_nbf, footer],\n",
|
||||
" layout=Layout(\n",
|
||||
" width='100%',\n",
|
||||
" grid_template_rows='auto auto auto',\n",
|
||||
" grid_template_columns='40% 20% 20% 20%',\n",
|
||||
" grid_template_columns='50% 20% 30%',\n",
|
||||
" grid_template_areas='''\n",
|
||||
" \"header header header header \"\n",
|
||||
" \"methods ctxaxis check1 check2\"\n",
|
||||
" \"gr_size ctxaxis check3 check5\"\n",
|
||||
" \". ctxaxis check4 . \" \n",
|
||||
" \"footer footer footer footer\"\n",
|
||||
" \"header header header \"\n",
|
||||
" \"methods ctxaxis check1 \"\n",
|
||||
" \"charts ctxaxis check2 \"\n",
|
||||
" \"gr_size ctxaxis check3 \"\n",
|
||||
" \". . check4 \"\n",
|
||||
" \". . check5 \"\n",
|
||||
" \"footer footer footer\"\n",
|
||||
" ''')\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"def ptycho_interact(beam, aperture, aperture_res, aperture_res2, probe, cl, matrix, defocus, mag, camera, binning, dwell_time, restriction, method, ctf_xaxis, cl_check_laa, cl_check_pix, cl_check_def, cl_check_1bf, cl_check_nbf, graph_size):\n",
|
||||
"def ptycho_interact(beam, aperture, aperture_res, aperture_res2, probe, cl, matrix, defocus, mag, camera, binning, dwell_time, restriction, method, ctf_xaxis, cl_check_laa, cl_check_pix, cl_check_def, cl_check_1bf, cl_check_nbf, graph_size, chart):\n",
|
||||
" \n",
|
||||
" ### SINGLE SETTING PARAMETERS ###\n",
|
||||
" wavelength = pty.get_wavelength(beam)*1e12\n",
|
||||
@ -464,59 +468,90 @@
|
||||
" pctf = pty.get_ssb_ctf()\n",
|
||||
" apertury = opt.apertures()\n",
|
||||
" \n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"\n",
|
||||
" \n",
|
||||
" ### SAMPLE PLANE ##########################################\n",
|
||||
" points = 5\n",
|
||||
" yyy = np.append(np.linspace(0,overlap,100), 200)\n",
|
||||
" wid = np.linspace(0,points-1,points) * step_size_corr\n",
|
||||
" wid = np.array([-2, -1, 0, 1, 2]) * step_size_corr\n",
|
||||
" \n",
|
||||
" fig5 = make_subplots(specs=[[{\"secondary_y\": True}]])\n",
|
||||
" fig5.update_xaxes(title_text=\"Sample plane (nm)\", range=[0, points*step_size_corr], showgrid=False, zeroline=False)\n",
|
||||
" fig5.update_yaxes(range=[0, points*step_size_corr],showgrid=False, showticklabels=False)\n",
|
||||
" fig5.update_xaxes(title_text=\"Sample plane (nm)\", range=[-4*step_size_corr, 4*step_size_corr], showgrid=False, zeroline=False)\n",
|
||||
" fig5.update_yaxes(range=[-4*step_size_corr, 4*step_size_corr],showgrid=False, showticklabels=False)\n",
|
||||
" for x in range(len(wid)):\n",
|
||||
" fig5.add_trace(go.Scatter(showlegend=False, x=wid, y=np.ones(len(wid))*wid[x], marker_color='blue'),secondary_y=False)\n",
|
||||
" for x in range(len(wid)): \n",
|
||||
" for y in range(len(wid)): \n",
|
||||
" fig5.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", opacity=0.1, fillcolor=\"#FF7F7F\",name=False, x0=wid[x]-beam_diameter/2, y0=wid[y]-beam_diameter/2, x1=wid[x]+beam_diameter/2, y1=wid[y]+beam_diameter/2, line_color=\"red\",secondary_y=False)\n",
|
||||
"\n",
|
||||
" fig5.add_trace(go.Scatter(showlegend=True, x=[-1], y=[-1],marker_size=12, marker_color='blue', name='Step '+str(np.round(10*step_size,3))+' Å ('+str(np.round(10*step_size_corr,3))+')'))\n",
|
||||
" fig5.add_annotation(x=-1*step_size_corr, y=-2*step_size_corr, ax=-2*step_size_corr, ay=-2*step_size_corr, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig5.add_annotation(x=-2*step_size_corr, y=-1*step_size_corr, ax=-2*step_size_corr, ay=-2*step_size_corr, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig5.add_annotation(x=-1.25*step_size_corr, y=-1.5*step_size_corr, text=str(np.round(10*step_size_corr,3))+' Å', showarrow=False, yshift=0)\n",
|
||||
" \n",
|
||||
" fig5.add_annotation(x=2*step_size_corr-0.75*beam_diameter/2, y=-2*step_size_corr-0.75*beam_diameter/2, ax=2*step_size_corr, ay=-2*step_size_corr,xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig5.add_annotation(x=2*step_size_corr+0.75*beam_diameter/2, y=-2*step_size_corr+0.75*beam_diameter/2, ax=2*step_size_corr, ay=-2*step_size_corr,xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig5.add_annotation(x=2.25*step_size_corr, y=-2*step_size_corr, text=str(np.round(10*beam_diameter,2))+' Å', showarrow=False, yshift=-15)\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" if method == 'direct':\n",
|
||||
" xx = 2*wavelength/(np.sin(semi_angle_corr*omega/1000))/100\n",
|
||||
" fig5.add_trace(go.Scatter(showlegend=True, x=[-1], y=[-1],marker_size=12, marker_color='green', name='Rec step '+str(np.round(xx[-1]/3,2))+' Å')) \n",
|
||||
" \n",
|
||||
" fig5.add_trace(go.Scatter(showlegend=True, x=[-1], y=[-1],marker_size=12, marker_color='#FF7F7F', name='Beam ⌀ '+ str(np.round(10*beam_diameter,2))+\" Å\"))\n",
|
||||
" fig5.update_layout(legend=dict(orientation=\"v\",yanchor=\"bottom\",y=0.85,xanchor=\"right\",x=0.9))\n",
|
||||
" fig5.add_trace(go.Scatter(showlegend=False, x = points*step_size_corr*np.ones(len(yyy)), y=yyy, opacity=1,mode='markers',marker_symbol = \"triangle-down\",marker=dict(size=20, color=yyy, colorscale='rainbow_r', showscale=False)),secondary_y=True) \n",
|
||||
" fig5.update_yaxes(title_text=\"Overlap %\", range=[0, 100],showgrid=False, showticklabels=True, tickvals = [0, 20, 40,50, 60,70, 80, 90, 100], secondary_y=True)\n",
|
||||
" fig5.update_layout(title={'text': \"Sample\",'y':0.95, 'x':0.30,'xanchor': 'left','yanchor': 'top'})\n",
|
||||
" fig5.add_trace(go.Scatter(showlegend=False, x = -4*step_size_corr*np.ones(len(yyy)), y=yyy, opacity=1,mode='markers',marker_symbol = \"triangle-down\",marker=dict(size=20, color=yyy, colorscale='rainbow_r', showscale=False)),secondary_y=True) \n",
|
||||
" fig5.update_yaxes(range=[0, 100], showgrid=False, showticklabels=False, secondary_y=True)\n",
|
||||
" fig5.update_yaxes(title_text=\"Overlap %\", showgrid=False, showticklabels=True, tickvals = [-4*step_size_corr, -2*step_size_corr, 0, 2*step_size_corr, 4*step_size_corr],ticktext = ['0', '25', '50', '75', '100'], secondary_y=False)\n",
|
||||
" fig5.update_layout(title={'text': \"Sample\",'y': 0.975, 'x': 0.30,'xanchor': 'left','yanchor': 'top'})\n",
|
||||
" fig5.update_layout(width=4.5*graph_size, height=3.0*graph_size, margin =dict(l=1.3*graph_size, r=0.3*graph_size, t=0.1*graph_size, b=0))\n",
|
||||
"\n",
|
||||
" \n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" ### DETECTOR PLANE ##########################################\n",
|
||||
" fig6 = go.Figure() \n",
|
||||
" fig6.update_xaxes(title_text=\"Pixels\", range=[1, num_pixels], zeroline=False)\n",
|
||||
" fig6.update_yaxes(range=[1, num_pixels], showticklabels=False,)\n",
|
||||
" for x in np.linspace(1,int(np.round(covered_alfas)),int(np.round(covered_alfas))):\n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", x0=num_pixels/2-x*beam_diameter_pix, y0=num_pixels/2-x*beam_diameter_pix, x1=num_pixels/2+x*beam_diameter_pix, y1=num_pixels/2+x*beam_diameter_pix,line_color=\"gray\")\n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=False,x=[num_pixels/2],y=[num_pixels/2-x*beam_diameter_pix],mode=\"lines+text\", text=str(int(2*x))+\"α\",textposition=\"top center\"))\n",
|
||||
" fig6 = make_subplots(specs=[[{\"secondary_y\": True}]])\n",
|
||||
" \n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", fillcolor=\"#FF7F7F\", x0=num_pixels/2-beam_diameter_pix/2, y0=num_pixels/2-beam_diameter_pix/2, x1=num_pixels/2+beam_diameter_pix/2, y1=num_pixels/2+beam_diameter_pix/2,line_color=\"#FF7F7F\")\n",
|
||||
" fig6.add_annotation(x=num_pixels/2-beam_diameter_pix/2, y=num_pixels/2, ax=num_pixels/2+beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=3,arrowsize=1,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig6.add_annotation(x=num_pixels/2+beam_diameter_pix/2,y=num_pixels/2, ax=num_pixels/2-beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y', text='', showarrow=True,arrowhead=3,arrowsize=1,arrowwidth=1,arrowcolor='black')\n",
|
||||
" for x in np.linspace(1,int(np.round(covered_alfas)),int(np.round(covered_alfas))):\n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\", x0=num_pixels/2-x*beam_diameter_pix, y0=num_pixels/2-x*beam_diameter_pix, x1=num_pixels/2+x*beam_diameter_pix, y1=num_pixels/2+x*beam_diameter_pix, line=dict(color=\"gray\",width=1,dash=\"dot\",),secondary_y=False)\n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=False,x=[num_pixels/2],y=[num_pixels/2+x*beam_diameter_pix],mode=\"lines+text\", text=str(int(2*x))+\"α\",textposition=\"top center\"),secondary_y=False)\n",
|
||||
" \n",
|
||||
" fig6.add_shape(type=\"circle\",xref=\"x\", yref=\"y\",opacity=0.5, fillcolor=\"#FF7F7F\", x0=num_pixels/2-beam_diameter_pix/2, y0=num_pixels/2-beam_diameter_pix/2, x1=num_pixels/2+beam_diameter_pix/2, y1=num_pixels/2+beam_diameter_pix/2,line_color=\"#FF7F7F\",secondary_y=False)\n",
|
||||
" fig6.add_annotation(x=num_pixels/2-beam_diameter_pix/2, y=num_pixels/2, ax=num_pixels/2+beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y',text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig6.add_annotation(x=num_pixels/2+beam_diameter_pix/2,y=num_pixels/2, ax=num_pixels/2-beam_diameter_pix/2, ay=num_pixels/2, xref='x',yref='y',axref='x',ayref='y', text='', showarrow=True,arrowhead=2,arrowsize=2,arrowwidth=1,arrowcolor='black')\n",
|
||||
" fig6.add_annotation(x=num_pixels/2, y=num_pixels/2, text=str(np.round(beam_diameter_pix,1))+\" pix\", showarrow=False, yshift=10)\n",
|
||||
" fig6.add_trace(go.Scatter(x=[1,1.5,1,1.5], y=[1,1,1.5,1.5], name='Pix ∠ ' +str(np.round(pixel_angle,2))+' mrad'))\n",
|
||||
" fig6.add_trace(go.Scatter(x=[1,1.5,1,1.5], y=[1,1,1.5,1.5], name='Pixel size ' +str(np.round(size_pixel,2))+' um'))\n",
|
||||
" fig6.update_layout(legend=dict(orientation=\"v\",yanchor=\"bottom\",y=0.80,xanchor=\"right\",x=1))\n",
|
||||
" fig6.update_layout(title={'text': \"Detector\",'y':0.95, 'x':0.11,'xanchor': 'left','yanchor': 'top'})\n",
|
||||
" fig6.update_layout(xaxis = dict(tickmode = 'array', tickvals = [1, num_pixels/4, num_pixels/2, 3*num_pixels/4, num_pixels])) \n",
|
||||
" fig6.update_layout(width=3.5*graph_size, height=3*graph_size, margin = dict(l=0.35*graph_size, r=0.65*graph_size, t=0.3*graph_size, b=0))\n",
|
||||
" fig6.add_annotation(x=num_pixels/2, y=num_pixels/2, text=\"1 pix = \"+str(np.round(pixel_angle,2))+\" mrad\", showarrow=False, yshift=-10)\n",
|
||||
" fig6.add_annotation(x=num_pixels/2, y=num_pixels/10, text=\"Real pixel size = \"+str(np.round(size_pixel,2))+\" μm\", showarrow=False, yshift=0)\n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=True,x=[-1], y=[-1], marker_color='red', name = \"BF disk\"),secondary_y=False)\n",
|
||||
" \n",
|
||||
" fig6.add_trace(go.Scatter(showlegend=False,x=[-1], y=[-1]),secondary_y=True)\n",
|
||||
" \n",
|
||||
" fig6.update_layout(legend=dict(orientation=\"h\",yanchor=\"bottom\",y=1.00,xanchor=\"right\",x=0.9))\n",
|
||||
" fig6.update_layout(title={'text': \"Detector\",'y':0.975, 'x':0.11,'xanchor': 'left','yanchor': 'top'})\n",
|
||||
" \n",
|
||||
" fig6.update_xaxes(title_text=\"Pixels\", range=[1, num_pixels], zeroline=False, tickvals = [1, num_pixels/4, num_pixels/2, 3*num_pixels/4, num_pixels]) \n",
|
||||
" fig6.update_yaxes(range=[1, num_pixels], showticklabels=False, showgrid=False, secondary_y=False)\n",
|
||||
" fig6.update_yaxes(title_text=\"Angular cover (mrad)\", range=[1, num_pixels], showticklabels=True, tickvals = [1, num_pixels/4, num_pixels/2, 3*num_pixels/4, num_pixels], ticktext = ['', np.round(detector_cover/4,1), np.round(detector_cover/2,1), np.round(3*detector_cover/4,1), np.round(detector_cover,1)], secondary_y=True) \n",
|
||||
" \n",
|
||||
" fig6.update_layout(width=3.5*graph_size, height=3*graph_size, margin = dict(l=0.35*graph_size, r=0.48*graph_size, t=0.3*graph_size, b=0))\n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" focusdepth = wavelength/(semi_angle_corr/1000)**2/1000\n",
|
||||
" ssb_cl, kolik = pty.cl4ssb(detector_cover_a_all)\n",
|
||||
" ### MICROSCOPE SCHEME ##########################################\n",
|
||||
@ -654,20 +689,27 @@
|
||||
" fig4.update_layout(xaxis = dict(tickmode = 'array', tickvals = opt.cameralengths()))\n",
|
||||
" fig4.update_layout(width=8.0*graph_size, height=2.25*graph_size, margin =dict(l=1.3*graph_size, r=0.25*graph_size, t=0.3*graph_size, b=0.3*graph_size))\n",
|
||||
"\n",
|
||||
" ### SHOWING ###\n",
|
||||
" right_column = VBox([go.FigureWidget(fig),HBox([go.FigureWidget(fig5),go.FigureWidget(fig6)]),go.FigureWidget(fig4)])\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" \n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" ### SHOWING ###\n",
|
||||
" if chart == 'micr':\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" total = HBox([left_column]) \n",
|
||||
" \n",
|
||||
" total = HBox([left_column, right_column])\n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px')\n",
|
||||
" \n",
|
||||
" elif chart == 'dedic':\n",
|
||||
" right_column = VBox([go.FigureWidget(fig) ,HBox([go.FigureWidget(fig5),go.FigureWidget(fig6)]),go.FigureWidget(fig4)])\n",
|
||||
" total = HBox([right_column])\n",
|
||||
" \n",
|
||||
" else: \n",
|
||||
" right_column = VBox([go.FigureWidget(fig) ,HBox([go.FigureWidget(fig5),go.FigureWidget(fig6)]),go.FigureWidget(fig4)])\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" total = HBox([left_column, right_column])\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px') \n",
|
||||
" display(total)\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
"\n",
|
||||
" \n",
|
||||
" \n",
|
||||
" if method == 'iterative': \n",
|
||||
@ -781,7 +823,7 @@
|
||||
" \n",
|
||||
" dictionary[i] = ToggleButtons(options=data_tuple, button_style=button_style, icons = icons, **align6)\n",
|
||||
" \n",
|
||||
" legend = ToggleButtons(options=['Ptycho pix. (Å)','Det. cover (mrad)','Det. cover (α)', 'Max. def. (nm)','Selected by CL ','Nominal CL (cm)',], \n",
|
||||
" legend = ToggleButtons(options=['Ptycho pixel (Å)','Det. cover (mrad)','Det. cover (α)', 'Max. def. (nm)','Selected by CL ','Nominal CL (cm)',], \n",
|
||||
" tooltips=['Dependent on: detector, beam energy, camera length',\n",
|
||||
" 'Dependent on: detector, camera length',\n",
|
||||
" 'Dependent on: detector, camera length, probe semi-angle',\n",
|
||||
@ -796,22 +838,32 @@
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" ### SHOWING ###\n",
|
||||
" sample_overlap = HBox([go.FigureWidget(fig5), go.FigureWidget(fig7), go.FigureWidget(fig6)]) \n",
|
||||
" right_column = VBox([HBox([go.FigureWidget(fig),checks]), sample_overlap, cltab]) \n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)]) \n",
|
||||
" \n",
|
||||
" \n",
|
||||
" total = HBox([left_column, right_column])\n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px')\n",
|
||||
" \n",
|
||||
" if chart == 'micr':\n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)])\n",
|
||||
" total = HBox([left_column]) \n",
|
||||
" \n",
|
||||
" elif chart == 'dedic':\n",
|
||||
" sample_overlap = HBox([go.FigureWidget(fig5), go.FigureWidget(fig7), go.FigureWidget(fig6)]) \n",
|
||||
" right_column = VBox([HBox([go.FigureWidget(fig),checks]), sample_overlap, cltab]) \n",
|
||||
" total = HBox([right_column])\n",
|
||||
" \n",
|
||||
" else: \n",
|
||||
" sample_overlap = HBox([go.FigureWidget(fig5), go.FigureWidget(fig7), go.FigureWidget(fig6)]) \n",
|
||||
" right_column = VBox([HBox([go.FigureWidget(fig),checks]), sample_overlap, cltab]) \n",
|
||||
" left_column = VBox([go.FigureWidget(fig8)]) \n",
|
||||
" total = HBox([left_column, right_column]) \n",
|
||||
" \n",
|
||||
" total.layout = Layout(border='solid 0px gray',margin='10px 10px 10px 40px', padding='10px 10px 10px 10px') \n",
|
||||
" display(total)\n",
|
||||
"\n",
|
||||
" \n",
|
||||
" return \n",
|
||||
" \n",
|
||||
"gui = interactive_output(ptycho_interact, {\"beam\": beam, \"aperture\": aperture,\"aperture_res\": aperture_res,\"aperture_res2\": aperture_res2, \"probe\": probe, \"cl\": cl, \"matrix\": matrix, \"defocus\": defocus, \"mag\": mag, \"camera\": camera,\n",
|
||||
" \"binning\": binning, \"dwell_time\": dwell_time, \"restriction\": restriction, \"method\": method, \"ctf_xaxis\": ctf_xaxis,\n",
|
||||
" \"cl_check_laa\":cl_check_laa, \"cl_check_pix\": cl_check_pix, \"cl_check_def\": cl_check_def, \"cl_check_1bf\": cl_check_1bf, \"cl_check_nbf\": cl_check_nbf, \"graph_size\": graph_size}) \n",
|
||||
" \"cl_check_laa\":cl_check_laa, \"cl_check_pix\": cl_check_pix, \"cl_check_def\": cl_check_def, \"cl_check_1bf\": cl_check_1bf, \"cl_check_nbf\": cl_check_nbf, \"graph_size\": graph_size,\"chart\": chart}) \n",
|
||||
"\n"
|
||||
]
|
||||
},
|
||||
@ -845,14 +897,14 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"execution_count": 390,
|
||||
"id": "7937f054-fcd0-4e67-a20f-7696f5903a94",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"application/vnd.jupyter.widget-view+json": {
|
||||
"model_id": "47642ef0d8b94bceb11f878293997c33",
|
||||
"model_id": "6f84c5e6c29142a9bb9db08cd48aefbd",
|
||||
"version_major": 2,
|
||||
"version_minor": 0
|
||||
},
|
||||
@ -865,6 +917,7 @@
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"\n",
|
||||
"display(HBox([controls, VBox([small_controls, gui]) ]))"
|
||||
]
|
||||
},
|
||||
@ -888,6 +941,139 @@
|
||||
"# import ipywidgets\n",
|
||||
"# print(\"Ipywidgets version \", ipywidgets.__version__)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "33727cb4-c3d7-4134-be89-f10b9922fbda",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 75,
|
||||
"id": "1cb358ba-42c4-420a-a0a6-0de425e670a6",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"Ipywidgets version 7.6.5\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"import ipywidgets\n",
|
||||
"print(\"Ipywidgets version \", ipywidgets.__version__)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "a52ff861-8243-4d39-b7da-1ee8fb0ee494",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "61970cec-8678-4edf-99f6-4f832d2aad8d",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"https://ipywidgets.readthedocs.io/en/latest/user_install.html"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 386,
|
||||
"id": "a4628def-4c43-456e-a93b-95952e2a3dea",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<ul>\n",
|
||||
"<li><b>DescriptionStyle:</b> BoundedFloatText, BoundedIntText, Checkbox, ColorPicker, Combobox, DatePicker, Dropdown, FloatText, HTML, HTMLMath, IntText, Label, Password, Play, RadioButtons, Select, SelectMultiple, SelectionRangeSlider, SelectionSlider, Text, Textarea, ToggleButton, Valid</li>\n",
|
||||
"<li><b>ButtonStyle:</b> Button, FileUpload</li>\n",
|
||||
"<li><b>SliderStyle:</b> FloatLogSlider, FloatRangeSlider, FloatSlider, IntRangeSlider, IntSlider</li>\n",
|
||||
"<li><b>ProgressStyle:</b> FloatProgress, IntProgress</li>\n",
|
||||
"<li><b>ToggleButtonsStyle:</b> ToggleButtons</li></ul>"
|
||||
],
|
||||
"text/plain": [
|
||||
"<IPython.core.display.HTML object>"
|
||||
]
|
||||
},
|
||||
"execution_count": 386,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"from collections import defaultdict\n",
|
||||
"from IPython.display import HTML\n",
|
||||
"import ipywidgets\n",
|
||||
"from pprint import pprint\n",
|
||||
"\n",
|
||||
"reverse_lut = defaultdict(set)\n",
|
||||
"styles = set()\n",
|
||||
"for export_name in dir(ipywidgets.widgets):\n",
|
||||
" export = getattr(ipywidgets.widgets, export_name)\n",
|
||||
" try:\n",
|
||||
" if issubclass(export, ipywidgets.Widget) and 'style' in export.class_trait_names():\n",
|
||||
" reverse_lut[export.style.klass.__name__].add(export.__name__)\n",
|
||||
" styles.add(export.style.klass)\n",
|
||||
" except TypeError:\n",
|
||||
" pass\n",
|
||||
"\n",
|
||||
"html = '<ul>'\n",
|
||||
"for style, widgets in reverse_lut.items():\n",
|
||||
" html = f\"{html}\\n<li><b>{style}:</b> {', '.join(sorted(widgets))}</li>\"\n",
|
||||
"html += \"</ul>\"\n",
|
||||
"HTML(html)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 74,
|
||||
"id": "54c1add7-f5ec-43f0-a447-e22dd03926a7",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<table>\n",
|
||||
"<tr><th>Attribute</th><th>ToggleButtonsStyle</th><th>ButtonStyle</th><th>DescriptionStyle</th><th>ProgressStyle</th><th>SliderStyle</th></tr><tr><td>description_width</td><td>✓</td><td></td><td>✓</td><td>✓</td><td>✓</td></tr><tr><td>button_width</td><td>✓</td><td></td><td></td><td></td><td></td></tr><tr><td>font_weight</td><td>✓</td><td>✓</td><td></td><td></td><td></td></tr><tr><td>bar_color</td><td></td><td></td><td></td><td>✓</td><td></td></tr><tr><td>handle_color</td><td></td><td></td><td></td><td></td><td>✓</td></tr><tr><td>button_color</td><td></td><td>✓</td><td></td><td></td><td></td></tr></table>"
|
||||
],
|
||||
"text/plain": [
|
||||
"<IPython.core.display.HTML object>"
|
||||
]
|
||||
},
|
||||
"execution_count": 74,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"attributes = defaultdict(set)\n",
|
||||
"base_traits = set(ipywidgets.Style.class_trait_names())\n",
|
||||
"\n",
|
||||
"for s in styles:\n",
|
||||
" for t in s.class_trait_names():\n",
|
||||
" if not t.startswith(\"_\") and t not in base_traits:\n",
|
||||
" attributes[s.__name__].add(t)\n",
|
||||
"all_attributes = set().union(*attributes.values())\n",
|
||||
"\n",
|
||||
"html = '<table>\\n'\n",
|
||||
"html = f\"{html}<tr><th>Attribute</th>{ ''.join(f'<th>{s}</th>' for s in attributes.keys()) }</tr>\"\n",
|
||||
"for a in all_attributes:\n",
|
||||
" html = f\"\"\"{html}<tr><td>{a}</td>{ ''.join(f'<td>{\"✓\" if a in attribs else \"\"}</td>' for attribs in attributes.values()) }</tr>\"\"\"\n",
|
||||
"html += \"</table>\"\n",
|
||||
"HTML(html)"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
|
||||
Reference in New Issue
Block a user