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Version 0.09

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rskoupy
2023-11-29 18:58:13 +01:00
parent 1c4addafc7
commit 6001316fd5
3 changed files with 38 additions and 12 deletions
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25
.ipynb_checkpoints/ptychoScopy-checkpoint.ipynb
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@ -349,7 +349,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 179, "execution_count": 200,
"id": "8055b802-cf83-4250-aea9-54e3e6b73db0", "id": "8055b802-cf83-4250-aea9-54e3e6b73db0",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@ -469,7 +469,7 @@
" fig.add_trace(go.Scatter(showlegend=False, x=d, y=pctf, marker_color='gray', name='SSB-CTF',))\n", " fig.add_trace(go.Scatter(showlegend=False, x=d, y=pctf, marker_color='gray', name='SSB-CTF',))\n",
" \n", " \n",
" fig.add_trace(go.Scatter(x=2*wavelength/(np.sin(semi_angle_corr*omega/1000))/100, y=pctf, marker_color='red', name=str(np.round(semi_angle_corr,2))+ ' mrad',))\n", " fig.add_trace(go.Scatter(x=2*wavelength/(np.sin(semi_angle_corr*omega/1000))/100, y=pctf, marker_color='red', name=str(np.round(semi_angle_corr,2))+ ' mrad',))\n",
" fig.update_xaxes(title_text=\"Real space distance (Å)\", range=[0, 2.5], type=\"log\", zeroline=False)\n", " fig.update_xaxes(title_text=\"Real space distance (Å)\", range=[0.0001, 2.5], type=\"log\", zeroline=False)\n",
" \n", " \n",
" fig.update_layout(legend=dict(orientation=\"h\",yanchor=\"bottom\",y=0.75,xanchor=\"right\",x=1))\n", " fig.update_layout(legend=dict(orientation=\"h\",yanchor=\"bottom\",y=0.75,xanchor=\"right\",x=1))\n",
" # fig3.update_layout(title={'text': \"CTF\",'y':0.93, 'x':0.12,'xanchor': 'left','yanchor': 'top'})\n", " # fig3.update_layout(title={'text': \"CTF\",'y':0.93, 'x':0.12,'xanchor': 'left','yanchor': 'top'})\n",
@ -606,8 +606,8 @@
" \n", " \n",
" focusdepth = widgets.Label(value = f'Depth of focus (nm) '+ str(np.round(wavelength/(semi_angle_corr/1000)**2/1000,1)), **align3) \n", " focusdepth = widgets.Label(value = f'Depth of focus (nm) '+ str(np.round(wavelength/(semi_angle_corr/1000)**2/1000,1)), **align3) \n",
" \n", " \n",
" checks = widgets.VBox([widgets.Label('Final checks'),check1,check2, check3,electron_dose,focusdepth, acquisition_time]) \n", " \n",
" checks.layout = widgets.Layout(border='dashed 1px gray',margin='30px 5px 5px 5px', padding='10px 10px 10px 10px')\n", "\n",
"\n", "\n",
"\n", "\n",
" ### METHODS ########################################## \n", " ### METHODS ########################################## \n",
@ -628,13 +628,26 @@
" fig4.update_layout(xaxis = dict(tickmode = 'array', tickvals = opt.cameralengths()))\n", " fig4.update_layout(xaxis = dict(tickmode = 'array', tickvals = opt.cameralengths()))\n",
" fig4.update_layout(width=800, height=225, margin =dict(l=110, r=30, t=30, b=30))\n", " fig4.update_layout(width=800, height=225, margin =dict(l=110, r=30, t=30, b=30))\n",
" \n", " \n",
" \n",
" checks = widgets.VBox([widgets.Label('Final checks'), electron_dose,focusdepth, acquisition_time]) \n",
" checks.layout = widgets.Layout(border='dashed 1px gray',margin='30px 5px 5px 5px', padding='10px 10px 10px 10px')\n",
" \n",
" \n",
" ### SHOWING ###\n", " ### SHOWING ###\n",
" right_column = widgets.VBox([go.FigureWidget(fig),go.FigureWidget(fig5),go.FigureWidget(fig4)])\n", " right_column = widgets.VBox([go.FigureWidget(fig),go.FigureWidget(fig5),go.FigureWidget(fig4)])\n",
" left_column = widgets.VBox([go.FigureWidget(fig8), go.FigureWidget(fig6)])\n", " left_column = widgets.VBox([go.FigureWidget(fig8), go.FigureWidget(fig6)])\n",
" display(widgets.HBox([left_column, right_column, checks]))\n", " display(widgets.HBox([left_column, right_column, checks]))\n",
" \n", " \n",
" \n",
" \n",
" \n",
" \n",
" if method == 'iterative':\n", " if method == 'iterative':\n",
" \n", " \n",
" checks = widgets.VBox([widgets.Label('Final checks'),check1, check2, check3,electron_dose,focusdepth, acquisition_time]) \n",
" checks.layout = widgets.Layout(border='dashed 1px gray',margin='30px 5px 5px 5px', padding='10px 10px 10px 10px')\n",
" \n",
" \n",
" ### PROBE WINDOW ##########################################\n", " ### PROBE WINDOW ##########################################\n",
" if beam_diameter < probe_window/2:\n", " if beam_diameter < probe_window/2:\n",
" color = \"green\"\n", " color = \"green\"\n",
@ -729,14 +742,14 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 180, "execution_count": 201,
"id": "7937f054-fcd0-4e67-a20f-7696f5903a94", "id": "7937f054-fcd0-4e67-a20f-7696f5903a94",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [
{ {
"data": { "data": {
"application/vnd.jupyter.widget-view+json": { "application/vnd.jupyter.widget-view+json": {
"model_id": "3ff56079396a4d12814896dd2a44263f", "model_id": "a6b2620a5190425a830b6176ed85a285",
"version_major": 2, "version_major": 2,
"version_minor": 0 "version_minor": 0
}, },

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calibrations.xlsx
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25
ptychoScopy.ipynb
View File

@ -349,7 +349,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 179, "execution_count": 200,
"id": "8055b802-cf83-4250-aea9-54e3e6b73db0", "id": "8055b802-cf83-4250-aea9-54e3e6b73db0",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@ -469,7 +469,7 @@
" fig.add_trace(go.Scatter(showlegend=False, x=d, y=pctf, marker_color='gray', name='SSB-CTF',))\n", " fig.add_trace(go.Scatter(showlegend=False, x=d, y=pctf, marker_color='gray', name='SSB-CTF',))\n",
" \n", " \n",
" fig.add_trace(go.Scatter(x=2*wavelength/(np.sin(semi_angle_corr*omega/1000))/100, y=pctf, marker_color='red', name=str(np.round(semi_angle_corr,2))+ ' mrad',))\n", " fig.add_trace(go.Scatter(x=2*wavelength/(np.sin(semi_angle_corr*omega/1000))/100, y=pctf, marker_color='red', name=str(np.round(semi_angle_corr,2))+ ' mrad',))\n",
" fig.update_xaxes(title_text=\"Real space distance (Å)\", range=[0, 2.5], type=\"log\", zeroline=False)\n", " fig.update_xaxes(title_text=\"Real space distance (Å)\", range=[0.0001, 2.5], type=\"log\", zeroline=False)\n",
" \n", " \n",
" fig.update_layout(legend=dict(orientation=\"h\",yanchor=\"bottom\",y=0.75,xanchor=\"right\",x=1))\n", " fig.update_layout(legend=dict(orientation=\"h\",yanchor=\"bottom\",y=0.75,xanchor=\"right\",x=1))\n",
" # fig3.update_layout(title={'text': \"CTF\",'y':0.93, 'x':0.12,'xanchor': 'left','yanchor': 'top'})\n", " # fig3.update_layout(title={'text': \"CTF\",'y':0.93, 'x':0.12,'xanchor': 'left','yanchor': 'top'})\n",
@ -606,8 +606,8 @@
" \n", " \n",
" focusdepth = widgets.Label(value = f'Depth of focus (nm) '+ str(np.round(wavelength/(semi_angle_corr/1000)**2/1000,1)), **align3) \n", " focusdepth = widgets.Label(value = f'Depth of focus (nm) '+ str(np.round(wavelength/(semi_angle_corr/1000)**2/1000,1)), **align3) \n",
" \n", " \n",
" checks = widgets.VBox([widgets.Label('Final checks'),check1,check2, check3,electron_dose,focusdepth, acquisition_time]) \n", " \n",
" checks.layout = widgets.Layout(border='dashed 1px gray',margin='30px 5px 5px 5px', padding='10px 10px 10px 10px')\n", "\n",
"\n", "\n",
"\n", "\n",
" ### METHODS ########################################## \n", " ### METHODS ########################################## \n",
@ -628,13 +628,26 @@
" fig4.update_layout(xaxis = dict(tickmode = 'array', tickvals = opt.cameralengths()))\n", " fig4.update_layout(xaxis = dict(tickmode = 'array', tickvals = opt.cameralengths()))\n",
" fig4.update_layout(width=800, height=225, margin =dict(l=110, r=30, t=30, b=30))\n", " fig4.update_layout(width=800, height=225, margin =dict(l=110, r=30, t=30, b=30))\n",
" \n", " \n",
" \n",
" checks = widgets.VBox([widgets.Label('Final checks'), electron_dose,focusdepth, acquisition_time]) \n",
" checks.layout = widgets.Layout(border='dashed 1px gray',margin='30px 5px 5px 5px', padding='10px 10px 10px 10px')\n",
" \n",
" \n",
" ### SHOWING ###\n", " ### SHOWING ###\n",
" right_column = widgets.VBox([go.FigureWidget(fig),go.FigureWidget(fig5),go.FigureWidget(fig4)])\n", " right_column = widgets.VBox([go.FigureWidget(fig),go.FigureWidget(fig5),go.FigureWidget(fig4)])\n",
" left_column = widgets.VBox([go.FigureWidget(fig8), go.FigureWidget(fig6)])\n", " left_column = widgets.VBox([go.FigureWidget(fig8), go.FigureWidget(fig6)])\n",
" display(widgets.HBox([left_column, right_column, checks]))\n", " display(widgets.HBox([left_column, right_column, checks]))\n",
" \n", " \n",
" \n",
" \n",
" \n",
" \n",
" if method == 'iterative':\n", " if method == 'iterative':\n",
" \n", " \n",
" checks = widgets.VBox([widgets.Label('Final checks'),check1, check2, check3,electron_dose,focusdepth, acquisition_time]) \n",
" checks.layout = widgets.Layout(border='dashed 1px gray',margin='30px 5px 5px 5px', padding='10px 10px 10px 10px')\n",
" \n",
" \n",
" ### PROBE WINDOW ##########################################\n", " ### PROBE WINDOW ##########################################\n",
" if beam_diameter < probe_window/2:\n", " if beam_diameter < probe_window/2:\n",
" color = \"green\"\n", " color = \"green\"\n",
@ -729,14 +742,14 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 180, "execution_count": 201,
"id": "7937f054-fcd0-4e67-a20f-7696f5903a94", "id": "7937f054-fcd0-4e67-a20f-7696f5903a94",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [
{ {
"data": { "data": {
"application/vnd.jupyter.widget-view+json": { "application/vnd.jupyter.widget-view+json": {
"model_id": "3ff56079396a4d12814896dd2a44263f", "model_id": "a6b2620a5190425a830b6176ed85a285",
"version_major": 2, "version_major": 2,
"version_minor": 0 "version_minor": 0
}, },