diff --git a/.ipynb_checkpoints/ptychoScopy-checkpoint.ipynb b/.ipynb_checkpoints/ptychoScopy-checkpoint.ipynb index a56273b..1b4f582 100644 --- a/.ipynb_checkpoints/ptychoScopy-checkpoint.ipynb +++ b/.ipynb_checkpoints/ptychoScopy-checkpoint.ipynb @@ -28,7 +28,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 15, "id": "7425242d-3c91-4c1e-a424-08625a38ee7a", "metadata": {}, "outputs": [], @@ -301,7 +301,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 22, "id": "8055b802-cf83-4250-aea9-54e3e6b73db0", "metadata": {}, "outputs": [ @@ -338,7 +338,7 @@ "cl = ToggleButtons(options=opt.cameralengths(), value=12, description='Nominal camera length (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'), style = {'description_width': '60px','button_width': str(100/len(opt.detectors())-len(opt.detectors()))+'%', 'font_weight': 'bold'})\n", "restriction = ToggleButtons(options=[('.',False), ('..',True)], value = False, description='PAAR',icons = ['times','check'], layout=Layout(width='auto', grid_area='camera_set2'),style = {'description_width': '80px','button_width': '48%', 'font_weight': 'bold'})\n", - "binning = ToggleButtons(options=[('.',1), ('2×2',2), ('4×4',4), ('6×6',6), ('8×8',8)], value=1, description='Binning', icons = ['times','',''], layout=Layout(width='auto', grid_area='camera_set3'), **ali)\n", + "binning = ToggleButtons(options=[('.',1), ('2×2',2), ('4×4',4), ('3×3',3), ('6×6',6), ('8×8',8), ('12×12',12), ('16×16',16), ('24×24',24), ('32×32',32), ('48×48',48)], value=1, description='Binning', icons = ['times','',''], layout=Layout(width='auto', grid_area='camera_set3'), **ali)\n", "\n", "beam_res = Label(value = f'λ (pm) '+ str(\"{:.1f}\".format(pty.get_wavelength(beam.value)*1e12)),layout=Layout(width='auto', grid_area='sidebar1'),)\n", "beam.observe(inte.show_wavelength, names='value') \n", @@ -458,7 +458,6 @@ " \n", "\n", " ### SAMPLE PLANE ##########################################\n", - " points = 5\n", " yyy = np.append(np.linspace(0,overlap,100), 200)\n", " wid = np.array([-2, -1, 0, 1, 2]) * step_size_corr\n", " fig5 = make_subplots(specs=[[{\"secondary_y\": True}]])\n", @@ -811,7 +810,7 @@ "id": "1e474cb7-5fd4-4113-a3fa-ddf5ca152ce5", "metadata": {}, "source": [ - "![title](./ptychoscopy_logo.png)\n", + "![title](./logo2.png)\n", "\n", "Jupyter based interactive data acquisition tool designed for appropriate ptychographic data collection. It computes nessesary characteristics which play crutial role in final data reconstruction. \n", "You can chose of **Direct methods** (mainly Single Side Band ptychography) or **Iterative reconstruction** which takes probe defocus into account. With this tool, you can check for probe CTF, scanning step size, probe overlap, detector camera length a proper angular range collection, reconstructed probe size and many more.\n", @@ -836,14 +835,14 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 23, "id": "7937f054-fcd0-4e67-a20f-7696f5903a94", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c62795511dd9485eba200c05200bbee1", + "model_id": "0a48e2bb85fd41a5931e183508ad4aa4", "version_major": 2, "version_minor": 0 }, diff --git a/calibrations.xlsx b/calibrations.xlsx index 4c10116..60ed35e 100644 Binary files a/calibrations.xlsx and b/calibrations.xlsx differ diff --git a/logo2.png b/logo2.png new file mode 100644 index 0000000..cba7a03 Binary files /dev/null and b/logo2.png differ diff --git a/ptychoScopy.ipynb b/ptychoScopy.ipynb index a56273b..1b4f582 100644 --- a/ptychoScopy.ipynb +++ b/ptychoScopy.ipynb @@ -28,7 +28,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 15, "id": "7425242d-3c91-4c1e-a424-08625a38ee7a", "metadata": {}, "outputs": [], @@ -301,7 +301,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 22, "id": "8055b802-cf83-4250-aea9-54e3e6b73db0", "metadata": {}, "outputs": [ @@ -338,7 +338,7 @@ "cl = ToggleButtons(options=opt.cameralengths(), value=12, description='Nominal camera length (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'), style = {'description_width': '60px','button_width': str(100/len(opt.detectors())-len(opt.detectors()))+'%', 'font_weight': 'bold'})\n", "restriction = ToggleButtons(options=[('.',False), ('..',True)], value = False, description='PAAR',icons = ['times','check'], layout=Layout(width='auto', grid_area='camera_set2'),style = {'description_width': '80px','button_width': '48%', 'font_weight': 'bold'})\n", - "binning = ToggleButtons(options=[('.',1), ('2×2',2), ('4×4',4), ('6×6',6), ('8×8',8)], value=1, description='Binning', icons = ['times','',''], layout=Layout(width='auto', grid_area='camera_set3'), **ali)\n", + "binning = ToggleButtons(options=[('.',1), ('2×2',2), ('4×4',4), ('3×3',3), ('6×6',6), ('8×8',8), ('12×12',12), ('16×16',16), ('24×24',24), ('32×32',32), ('48×48',48)], value=1, description='Binning', icons = ['times','',''], layout=Layout(width='auto', grid_area='camera_set3'), **ali)\n", "\n", "beam_res = Label(value = f'λ (pm) '+ str(\"{:.1f}\".format(pty.get_wavelength(beam.value)*1e12)),layout=Layout(width='auto', grid_area='sidebar1'),)\n", "beam.observe(inte.show_wavelength, names='value') \n", @@ -458,7 +458,6 @@ " \n", "\n", " ### SAMPLE PLANE ##########################################\n", - " points = 5\n", " yyy = np.append(np.linspace(0,overlap,100), 200)\n", " wid = np.array([-2, -1, 0, 1, 2]) * step_size_corr\n", " fig5 = make_subplots(specs=[[{\"secondary_y\": True}]])\n", @@ -811,7 +810,7 @@ "id": "1e474cb7-5fd4-4113-a3fa-ddf5ca152ce5", "metadata": {}, "source": [ - "![title](./ptychoscopy_logo.png)\n", + "![title](./logo2.png)\n", "\n", "Jupyter based interactive data acquisition tool designed for appropriate ptychographic data collection. It computes nessesary characteristics which play crutial role in final data reconstruction. \n", "You can chose of **Direct methods** (mainly Single Side Band ptychography) or **Iterative reconstruction** which takes probe defocus into account. With this tool, you can check for probe CTF, scanning step size, probe overlap, detector camera length a proper angular range collection, reconstructed probe size and many more.\n", @@ -836,14 +835,14 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 23, "id": "7937f054-fcd0-4e67-a20f-7696f5903a94", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c62795511dd9485eba200c05200bbee1", + "model_id": "0a48e2bb85fd41a5931e183508ad4aa4", "version_major": 2, "version_minor": 0 }, diff --git a/ptychoscopy_logo.png b/ptychoscopy_logo.png deleted file mode 100644 index d1e817f..0000000 Binary files a/ptychoscopy_logo.png and /dev/null differ