SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/binning/binning.html b/sed/develop/_modules/sed/binning/binning.html index 63cd867..b4878b5 100644 --- a/sed/develop/_modules/sed/binning/binning.html +++ b/sed/develop/_modules/sed/binning/binning.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/binning/numba_bin.html b/sed/develop/_modules/sed/binning/numba_bin.html index dc45cdd..fbfbc86 100644 --- a/sed/develop/_modules/sed/binning/numba_bin.html +++ b/sed/develop/_modules/sed/binning/numba_bin.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/binning/utils.html b/sed/develop/_modules/sed/binning/utils.html index 2d28433..5027071 100644 --- a/sed/develop/_modules/sed/binning/utils.html +++ b/sed/develop/_modules/sed/binning/utils.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/calibrator/delay.html b/sed/develop/_modules/sed/calibrator/delay.html index 4f55c31..bd07c82 100644 --- a/sed/develop/_modules/sed/calibrator/delay.html +++ b/sed/develop/_modules/sed/calibrator/delay.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/calibrator/energy.html b/sed/develop/_modules/sed/calibrator/energy.html index 8943c49..52e7777 100644 --- a/sed/develop/_modules/sed/calibrator/energy.html +++ b/sed/develop/_modules/sed/calibrator/energy.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/calibrator/momentum.html b/sed/develop/_modules/sed/calibrator/momentum.html index 7ade4f4..96cff5c 100644 --- a/sed/develop/_modules/sed/calibrator/momentum.html +++ b/sed/develop/_modules/sed/calibrator/momentum.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/core/config.html b/sed/develop/_modules/sed/core/config.html index 432f079..426bb3b 100644 --- a/sed/develop/_modules/sed/core/config.html +++ b/sed/develop/_modules/sed/core/config.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/core/dfops.html b/sed/develop/_modules/sed/core/dfops.html index 712c1f0..768fff6 100644 --- a/sed/develop/_modules/sed/core/dfops.html +++ b/sed/develop/_modules/sed/core/dfops.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/core/metadata.html b/sed/develop/_modules/sed/core/metadata.html index 6a30594..7d40544 100644 --- a/sed/develop/_modules/sed/core/metadata.html +++ b/sed/develop/_modules/sed/core/metadata.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/core/processor.html b/sed/develop/_modules/sed/core/processor.html index e80aae3..4d869ef 100644 --- a/sed/develop/_modules/sed/core/processor.html +++ b/sed/develop/_modules/sed/core/processor.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/dataset/dataset.html b/sed/develop/_modules/sed/dataset/dataset.html index 60acaf0..6aa2736 100644 --- a/sed/develop/_modules/sed/dataset/dataset.html +++ b/sed/develop/_modules/sed/dataset/dataset.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/diagnostics.html b/sed/develop/_modules/sed/diagnostics.html index 4a134a4..151926e 100644 --- a/sed/develop/_modules/sed/diagnostics.html +++ b/sed/develop/_modules/sed/diagnostics.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/io/hdf5.html b/sed/develop/_modules/sed/io/hdf5.html index 5362944..a234ea2 100644 --- a/sed/develop/_modules/sed/io/hdf5.html +++ b/sed/develop/_modules/sed/io/hdf5.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/io/nexus.html b/sed/develop/_modules/sed/io/nexus.html index 91b9c7e..401b1bf 100644 --- a/sed/develop/_modules/sed/io/nexus.html +++ b/sed/develop/_modules/sed/io/nexus.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/io/tiff.html b/sed/develop/_modules/sed/io/tiff.html index 96e2e04..9877841 100644 --- a/sed/develop/_modules/sed/io/tiff.html +++ b/sed/develop/_modules/sed/io/tiff.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/loader/base/loader.html b/sed/develop/_modules/sed/loader/base/loader.html index f5c6002..0b8a280 100644 --- a/sed/develop/_modules/sed/loader/base/loader.html +++ b/sed/develop/_modules/sed/loader/base/loader.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/loader/flash/loader.html b/sed/develop/_modules/sed/loader/flash/loader.html index 0b94508..ed40b62 100644 --- a/sed/develop/_modules/sed/loader/flash/loader.html +++ b/sed/develop/_modules/sed/loader/flash/loader.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/loader/flash/metadata.html b/sed/develop/_modules/sed/loader/flash/metadata.html index 9bcc09b..6624bb3 100644 --- a/sed/develop/_modules/sed/loader/flash/metadata.html +++ b/sed/develop/_modules/sed/loader/flash/metadata.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/loader/generic/loader.html b/sed/develop/_modules/sed/loader/generic/loader.html index 9631aee..b7ed527 100644 --- a/sed/develop/_modules/sed/loader/generic/loader.html +++ b/sed/develop/_modules/sed/loader/generic/loader.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/loader/loader_interface.html b/sed/develop/_modules/sed/loader/loader_interface.html index 4ffd324..4ac3f6b 100644 --- a/sed/develop/_modules/sed/loader/loader_interface.html +++ b/sed/develop/_modules/sed/loader/loader_interface.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/loader/mirrorutil.html b/sed/develop/_modules/sed/loader/mirrorutil.html index bd08a53..40b3367 100644 --- a/sed/develop/_modules/sed/loader/mirrorutil.html +++ b/sed/develop/_modules/sed/loader/mirrorutil.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/loader/mpes/loader.html b/sed/develop/_modules/sed/loader/mpes/loader.html index 77a8118..0cc433c 100644 --- a/sed/develop/_modules/sed/loader/mpes/loader.html +++ b/sed/develop/_modules/sed/loader/mpes/loader.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/_modules/sed/loader/sxp/loader.html b/sed/develop/_modules/sed/loader/sxp/loader.html index e4dea26..651fea9 100644 --- a/sed/develop/_modules/sed/loader/sxp/loader.html +++ b/sed/develop/_modules/sed/loader/sxp/loader.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_modules/sed/loader/utils.html b/sed/develop/_modules/sed/loader/utils.html index cb3d7da..b7878df 100644 --- a/sed/develop/_modules/sed/loader/utils.html +++ b/sed/develop/_modules/sed/loader/utils.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/_sources/tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb.txt b/sed/develop/_sources/tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb.txt index 5dd7691..5391439 100644 --- a/sed/develop/_sources/tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb.txt +++ b/sed/develop/_sources/tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb.txt @@ -238,7 +238,7 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "res.plot(robust=True, ax=ax[0], cmap='terrain')\n", "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n", "ax[0].set_title('raw')\n", @@ -338,7 +338,7 @@ "outputs": [], "source": [ "\n", - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "res_bam.sel(bam=slice(-6400,-5100)).sum('trainId').plot(ax=ax[0],robust=True, cmap='terrain')\n", "res_bam.sel(bam=slice(-6400,-5100)).sum('pulseId').plot(ax=ax[1],robust=True, cmap='terrain')\n", "plt.show()" @@ -404,7 +404,7 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n", "res_corr.plot(robust=True, ax=ax[0], cmap='terrain')\n", "ax[0].set_title('raw')\n", @@ -497,7 +497,7 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax=plt.subplots(2,2,figsize=(6,8),layout=\"constrained\")\n", + "fig,ax=plt.subplots(2,2,figsize=(6,6),layout=\"constrained\")\n", "\n", "plt.axes(ax[0,0])\n", "res.plot(cmap='terrain', robust=True)\n", diff --git a/sed/develop/_sources/tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb.txt b/sed/develop/_sources/tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb.txt index 843fd97..b8be7a4 100644 --- a/sed/develop/_sources/tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb.txt +++ b/sed/develop/_sources/tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb.txt @@ -327,7 +327,7 @@ "bins = [100,60]\n", "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")\n", "\n", - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n", "res_corr.plot(ax=ax[0], cmap='terrain')\n", "ax[0].set_title('raw')\n", @@ -443,7 +443,7 @@ "bins = [200,60]\n", "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")\n", "\n", - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n", "res_corr.plot(ax=ax[0], cmap='terrain')\n", "ax[0].set_title('raw')\n", diff --git a/sed/develop/_sources/tutorial/4_hextof_workflow.ipynb.txt b/sed/develop/_sources/tutorial/4_hextof_workflow.ipynb.txt index 6019dd8..847051f 100644 --- a/sed/develop/_sources/tutorial/4_hextof_workflow.ipynb.txt +++ b/sed/develop/_sources/tutorial/4_hextof_workflow.ipynb.txt @@ -345,10 +345,10 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,3,figsize=(6,4), layout='tight')\n", - "res_chessy.plot(ax=ax[0], robust=True)\n", - "res_t05.plot(ax=ax[1], robust=True)\n", - "res_t10.plot(ax=ax[2], robust=True)" + "fig,ax = plt.subplots(1,3,figsize=(6,2), layout='tight')\n", + "res_chessy.plot(ax=ax[0], robust=True, add_colorbar=False)\n", + "res_t05.plot(ax=ax[1], robust=True, add_colorbar=False)\n", + "res_t10.plot(ax=ax[2], robust=True, add_colorbar=False)" ] }, { @@ -759,7 +759,7 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "res.plot(robust=True, ax=ax[0])\n", "bg = res.isel(delayStage=slice(0,10)).mean('delayStage')\n", "(res-bg).plot(robust=True, ax=ax[1])" @@ -827,7 +827,7 @@ }, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,2,figsize=(6,4))\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3))\n", "res.plot(robust=True, ax=ax[0])\n", "bg = res.sel(delayStage=slice(-1,-0.2)).mean('delayStage')\n", "(res-bg).plot(robust=True, ax=ax[1])\n", @@ -848,7 +848,7 @@ "outputs": [], "source": [ "res = sp.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")\n", - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "res.plot(robust=True, ax=ax[0])\n", "bg = res.sel(delayStage=slice(-1,-.2)).mean('delayStage')\n", "(res-bg).plot(robust=True, ax=ax[1])" @@ -966,7 +966,7 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "res.plot(robust=True, ax=ax[0])\n", "bg = res.sel(delayStage=slice(-1,-.2)).mean('delayStage')\n", "(res-bg).plot(robust=True, ax=ax[1])" diff --git a/sed/develop/_sources/tutorial/9_hextof_workflow_trXPD.ipynb.txt b/sed/develop/_sources/tutorial/9_hextof_workflow_trXPD.ipynb.txt index af8b945..de017ee 100644 --- a/sed/develop/_sources/tutorial/9_hextof_workflow_trXPD.ipynb.txt +++ b/sed/develop/_sources/tutorial/9_hextof_workflow_trXPD.ipynb.txt @@ -291,7 +291,7 @@ "metadata": {}, "outputs": [], "source": [ - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n", "res_corr.plot(robust=True, ax=ax[0], cmap='terrain')\n", "ax[0].set_title('raw')\n", @@ -341,7 +341,7 @@ "plt.show()\n", "\n", "## XPD plots\n", - "fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')\n", + "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n", "res_kx_ky.sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')\n", "ax[0,0].set_title(\"XPD of $1^{st}$ order sidebands\")\n", "res_kx_ky.sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')\n", @@ -381,7 +381,7 @@ "## Apply Gaussian Blur to background image\n", "bgd_blur = xr.apply_ufunc(gaussian_filter, bgd, 15)\n", "\n", - "fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')\n", + "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n", "bgd.plot(robust=True, cmap='terrain', ax=ax[0])\n", "ax[0].set_title('Background image')\n", "bgd_blur.plot(cmap='terrain', ax=ax[1])\n", @@ -397,7 +397,7 @@ "outputs": [], "source": [ "## XPD normalized by background image\n", - "fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')\n", + "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n", "(res_kx_ky/bgd).sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')\n", "(res_kx_ky/bgd).sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')\n", "(res_kx_ky/bgd).sel(energy=slice(-33.6,-33.4)).mean('energy').plot(robust=True, ax=ax[1,0], cmap='terrain')\n", @@ -405,7 +405,7 @@ "fig.suptitle(f'Run {run_number}: XPD patterns after background normalization',fontsize='18')\n", "\n", "## XPD normalized by Gaussian-blurred background image\n", - "fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')\n", + "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n", "(res_kx_ky/bgd_blur).sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')\n", "(res_kx_ky/bgd_blur).sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')\n", "(res_kx_ky/bgd_blur).sel(energy=slice(-33.6,-33.4)).mean('energy').plot(robust=True, ax=ax[1,0], cmap='terrain')\n", @@ -413,7 +413,7 @@ "fig.suptitle(f'Run {run_number}: XPD patterns after Gaussian-blurred background normalization',fontsize='18')\n", "\n", "## XPD normalized by Gaussian-blurred background image and blurred to improve contrast\n", - "fig,ax = plt.subplots(2,2,figsize=(9,7), layout='constrained')\n", + "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n", "(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')\n", "(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')\n", "(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-33.6,-33.4)).mean('energy').plot(robust=True, ax=ax[1,0], cmap='terrain')\n", @@ -451,7 +451,7 @@ "W_5p_blur = xr.apply_ufunc(gaussian_filter, W_5p, 15)\n", "\n", "### Visualize results\n", - "fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')\n", + "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n", "(SB/SB_blur).plot(robust=True, ax=ax[0,0], cmap='terrain')\n", "(W_4f_7/W_4f_7_blur).plot(robust=True, ax=ax[0,1], cmap='terrain')\n", "(W_4f_5/W_4f_5_blur).plot(robust=True, ax=ax[1,0], cmap='terrain')\n", @@ -465,7 +465,7 @@ "W_5p_norm = xr.apply_ufunc(gaussian_filter, W_5p/W_5p_blur, 1)\n", "\n", "### Visualize results\n", - "fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')\n", + "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n", "SB_norm.plot(robust=True, ax=ax[0,0], cmap='terrain')\n", "W_4f_7_norm.plot(robust=True, ax=ax[0,1], cmap='terrain')\n", "W_4f_5_norm.plot(robust=True, ax=ax[1,0], cmap='terrain')\n", diff --git a/sed/develop/_static/documentation_options.js b/sed/develop/_static/documentation_options.js index 0ad4afd..950b52e 100644 --- a/sed/develop/_static/documentation_options.js +++ b/sed/develop/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '1.0.0a1.dev14+g568085b', + VERSION: '1.0.0a1.dev15+gb3e949f', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/sed/develop/genindex.html b/sed/develop/genindex.html index aab57c6..6a2ccf8 100644 --- a/sed/develop/genindex.html +++ b/sed/develop/genindex.html @@ -7,7 +7,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/index.html b/sed/develop/index.html index b75a899..8b96c40 100644 --- a/sed/develop/index.html +++ b/sed/develop/index.html @@ -9,7 +9,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/misc/contributing.html b/sed/develop/misc/contributing.html index f12fb0d..f212d7f 100644 --- a/sed/develop/misc/contributing.html +++ b/sed/develop/misc/contributing.html @@ -8,7 +8,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/misc/contribution.html b/sed/develop/misc/contribution.html index d5f068b..82da39d 100644 --- a/sed/develop/misc/contribution.html +++ b/sed/develop/misc/contribution.html @@ -8,7 +8,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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"sed.loader.sxp.loader.SXPLoader.create_multi_index_per_pulse", false]], "create_numpy_array_per_channel() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.create_numpy_array_per_channel", false]], "data_name (sed.dataset.dataset.dataset property)": [[9, "sed.dataset.dataset.Dataset.data_name", false]], "dataframe (sed.core.sedprocessor property)": [[8, "sed.core.SedProcessor.dataframe", false]], "dataset (class in sed.dataset.dataset)": [[9, "sed.dataset.dataset.Dataset", false]], "datasetsmanager (class in sed.dataset.dataset)": [[9, "sed.dataset.dataset.DatasetsManager", false]], "define_features() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.define_features", false]], "delaycalibrator (class in sed.calibrator.delay)": [[6, "sed.calibrator.delay.DelayCalibrator", false]], "detector_coordinates_2_k_coordinates() (in module sed.calibrator.momentum)": [[6, "sed.calibrator.momentum.detector_coordinates_2_k_coordinates", false]], "dictmerge() (in module sed.calibrator.momentum)": [[6, "sed.calibrator.momentum.dictmerge", false]], "drop_column() (in module sed.core.dfops)": [[10, "sed.core.dfops.drop_column", false]], "dup (sed.calibrator.energy.energycalibrator property)": [[6, "sed.calibrator.energy.EnergyCalibrator.dup", false]], "duplicateentryerror": [[14, "sed.core.metadata.DuplicateEntryError", false]], "energycalibrator (class in sed.calibrator.energy)": [[6, "sed.calibrator.energy.EnergyCalibrator", false]], "existing_data_paths (sed.dataset.dataset.dataset property)": [[9, "sed.dataset.dataset.Dataset.existing_data_paths", false]], "extract_bias() (in module sed.calibrator.energy)": [[6, "sed.calibrator.energy.extract_bias", false]], "extract_delay_stage_parameters() (in module sed.calibrator.delay)": [[6, "sed.calibrator.delay.extract_delay_stage_parameters", false]], "feature_extract() (sed.calibrator.energy.energycalibrator method)": [[6, "sed.calibrator.energy.EnergyCalibrator.feature_extract", false]], "feature_extract() (sed.calibrator.momentum.momentumcorrector method)": [[6, "sed.calibrator.momentum.MomentumCorrector.feature_extract", false]], "feature_select() (sed.calibrator.momentum.momentumcorrector method)": [[6, "sed.calibrator.momentum.MomentumCorrector.feature_select", false]], "features (sed.calibrator.momentum.momentumcorrector property)": [[6, "sed.calibrator.momentum.MomentumCorrector.features", false]], "filename (sed.dataset.dataset.datasetsmanager attribute)": [[9, "sed.dataset.dataset.DatasetsManager.FILENAME", false]], "files (sed.core.sedprocessor property)": [[8, "sed.core.SedProcessor.files", false]], "filter_column() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.filter_column", false]], "find_bias_peaks() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.find_bias_peaks", false]], "find_correspondence() (in module sed.calibrator.energy)": [[6, "sed.calibrator.energy.find_correspondence", false]], "find_nearest() (in module sed.calibrator.energy)": [[6, "sed.calibrator.energy.find_nearest", false]], "fit_energy_calibration() (in module sed.calibrator.energy)": [[6, "sed.calibrator.energy.fit_energy_calibration", false]], "flashloader (class in sed.loader.flash.loader)": [[13, "sed.loader.flash.loader.FlashLoader", false]], "forward_fill_lazy() (in module sed.core.dfops)": [[10, "sed.core.dfops.forward_fill_lazy", false]], "gather_calibration_metadata() (sed.calibrator.energy.energycalibrator method)": [[6, "sed.calibrator.energy.EnergyCalibrator.gather_calibration_metadata", false]], "gather_calibration_metadata() (sed.calibrator.momentum.momentumcorrector method)": [[6, "sed.calibrator.momentum.MomentumCorrector.gather_calibration_metadata", false]], "gather_correction_metadata() (sed.calibrator.energy.energycalibrator method)": [[6, "sed.calibrator.energy.EnergyCalibrator.gather_correction_metadata", false]], "gather_correction_metadata() (sed.calibrator.momentum.momentumcorrector method)": [[6, "sed.calibrator.momentum.MomentumCorrector.gather_correction_metadata", false]], "gather_files() (in module sed.loader.utils)": [[13, "sed.loader.utils.gather_files", false]], "gather_metadata() (sed.loader.mpes.loader.mpesloader method)": [[13, "sed.loader.mpes.loader.MpesLoader.gather_metadata", false]], "gather_metadata() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.gather_metadata", false]], "generate_inverse_dfield() (in module sed.calibrator.momentum)": [[6, "sed.calibrator.momentum.generate_inverse_dfield", false]], "generate_splinewarp() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.generate_splinewarp", false]], "genericloader (class in sed.loader.generic.loader)": [[13, "sed.loader.generic.loader.GenericLoader", false]], "get() (sed.dataset.dataset.dataset method)": [[9, "sed.dataset.dataset.Dataset.get", false]], "get_archiver_data() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.get_archiver_data", false]], "get_attribute() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.get_attribute", false]], "get_channels() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.get_channels", false]], "get_count_rate() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.get_count_rate", false]], "get_count_rate() (sed.loader.base.loader.baseloader method)": [[13, "sed.loader.base.loader.BaseLoader.get_count_rate", false]], "get_count_rate() (sed.loader.flash.loader.flashloader method)": [[13, "sed.loader.flash.loader.FlashLoader.get_count_rate", false]], "get_count_rate() (sed.loader.generic.loader.genericloader method)": [[13, "sed.loader.generic.loader.GenericLoader.get_count_rate", false]], "get_count_rate() (sed.loader.mpes.loader.mpesloader method)": [[13, "sed.loader.mpes.loader.MpesLoader.get_count_rate", false]], "get_count_rate() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.get_count_rate", false]], "get_datasets_and_aliases() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.get_datasets_and_aliases", false]], "get_elapsed_time() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.get_elapsed_time", false]], "get_elapsed_time() (sed.loader.base.loader.baseloader method)": [[13, "sed.loader.base.loader.BaseLoader.get_elapsed_time", false]], "get_elapsed_time() (sed.loader.flash.loader.flashloader method)": [[13, "sed.loader.flash.loader.FlashLoader.get_elapsed_time", false]], "get_elapsed_time() (sed.loader.generic.loader.genericloader method)": [[13, "sed.loader.generic.loader.GenericLoader.get_elapsed_time", false]], "get_elapsed_time() (sed.loader.mpes.loader.mpesloader method)": [[13, "sed.loader.mpes.loader.MpesLoader.get_elapsed_time", false]], "get_elapsed_time() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.get_elapsed_time", false]], "get_files_from_run_id() (sed.loader.base.loader.baseloader method)": [[13, "sed.loader.base.loader.BaseLoader.get_files_from_run_id", false]], "get_files_from_run_id() (sed.loader.flash.loader.flashloader method)": [[13, "sed.loader.flash.loader.FlashLoader.get_files_from_run_id", false]], "get_files_from_run_id() (sed.loader.generic.loader.genericloader method)": [[13, "sed.loader.generic.loader.GenericLoader.get_files_from_run_id", false]], "get_files_from_run_id() (sed.loader.mpes.loader.mpesloader method)": [[13, "sed.loader.mpes.loader.MpesLoader.get_files_from_run_id", false]], "get_files_from_run_id() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.get_files_from_run_id", false]], "get_loader() (in module sed.loader.loader_interface)": [[13, "sed.loader.loader_interface.get_loader", false]], "get_metadata() (sed.loader.flash.metadata.metadataretriever method)": [[13, "sed.loader.flash.metadata.MetadataRetriever.get_metadata", false]], "get_names_of_all_loaders() (in module sed.loader.loader_interface)": [[13, "sed.loader.loader_interface.get_names_of_all_loaders", false]], "get_normalization_histogram() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.get_normalization_histogram", false]], "get_parquet_metadata() (in module sed.loader.utils)": [[13, "sed.loader.utils.get_parquet_metadata", false]], "get_start_and_end_time() (sed.loader.mpes.loader.mpesloader method)": [[13, "sed.loader.mpes.loader.MpesLoader.get_start_and_end_time", false]], "get_stats() (in module sed.loader.utils)": [[13, "sed.loader.utils.get_stats", false]], "get_target_dir() (in module sed.loader.mirrorutil)": [[13, "sed.loader.mirrorutil.get_target_dir", false]], "grid_histogram() (in module sed.diagnostics)": [[11, "sed.diagnostics.grid_histogram", false]], "hdf5_to_array() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.hdf5_to_array", false]], "hdf5_to_dataframe() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.hdf5_to_dataframe", false]], "hdf5_to_timed_array() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.hdf5_to_timed_array", false]], "hdf5_to_timed_dataframe() (in module sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.hdf5_to_timed_dataframe", false]], "json_path (sed.dataset.dataset.datasetsmanager attribute)": [[9, "sed.dataset.dataset.DatasetsManager.json_path", false]], "load() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.load", false]], "load_bias_series() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.load_bias_series", false]], "load_config() (in module sed.core.config)": [[7, "sed.core.config.load_config", false]], "load_data() (sed.calibrator.energy.energycalibrator method)": [[6, "sed.calibrator.energy.EnergyCalibrator.load_data", false]], "load_data() (sed.calibrator.momentum.momentumcorrector method)": [[6, "sed.calibrator.momentum.MomentumCorrector.load_data", false]], "load_datasets_dict() 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[[10, "sed.core.dfops.map_columns_2d", false]], "metadata (sed.core.metadata.metahandler property)": [[14, "sed.core.metadata.MetaHandler.metadata", false]], "metadataretriever (class in sed.loader.flash.metadata)": [[13, "sed.loader.flash.metadata.MetadataRetriever", false]], "metahandler (class in sed.core.metadata)": [[14, "sed.core.metadata.MetaHandler", false]], "mm_to_ps() (in module sed.calibrator.delay)": [[6, "sed.calibrator.delay.mm_to_ps", false]], "module": [[5, "module-sed.binning", false], [5, "module-sed.binning.numba_bin", false], [5, "module-sed.binning.utils", false], [6, "module-sed.calibrator.delay", false], [6, "module-sed.calibrator.energy", false], [6, "module-sed.calibrator.momentum", false], [7, "module-sed.core.config", false], [8, "module-sed.core", false], [9, "module-sed.dataset.dataset", false], [10, "module-sed.core.dfops", false], [11, "module-sed.diagnostics", false], [12, "module-sed.io", false], [13, "module-sed.loader.base.loader", false], [13, "module-sed.loader.flash.loader", false], [13, "module-sed.loader.flash.metadata", false], [13, "module-sed.loader.generic.loader", false], [13, "module-sed.loader.loader_interface", false], [13, "module-sed.loader.mirrorutil", false], [13, "module-sed.loader.mpes.loader", false], [13, "module-sed.loader.sxp.loader", false], [13, "module-sed.loader.utils", false], [14, "module-sed.core.metadata", false]], "momentumcorrector (class in sed.calibrator.momentum)": [[6, "sed.calibrator.momentum.MomentumCorrector", false]], "mpesloader (class in sed.loader.mpes.loader)": [[13, "sed.loader.mpes.loader.MpesLoader", false]], "mycopy() (in module sed.loader.mirrorutil)": [[13, "sed.loader.mirrorutil.mycopy", false]], "mymakedirs() (in module sed.loader.mirrorutil)": [[13, "sed.loader.mirrorutil.mymakedirs", false]], "name (sed.dataset.dataset.datasetsmanager attribute)": [[9, "sed.dataset.dataset.DatasetsManager.NAME", false]], "normalization_histogram (sed.core.sedprocessor property)": [[8, 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"pre_binning() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.pre_binning", false]], "range_convert() (in module sed.calibrator.energy)": [[6, "sed.calibrator.energy.range_convert", false]], "read_dataframe() (sed.loader.base.loader.baseloader method)": [[13, "sed.loader.base.loader.BaseLoader.read_dataframe", false]], "read_dataframe() (sed.loader.flash.loader.flashloader method)": [[13, "sed.loader.flash.loader.FlashLoader.read_dataframe", false]], "read_dataframe() (sed.loader.generic.loader.genericloader method)": [[13, "sed.loader.generic.loader.GenericLoader.read_dataframe", false]], "read_dataframe() (sed.loader.mpes.loader.mpesloader method)": [[13, "sed.loader.mpes.loader.MpesLoader.read_dataframe", false]], "read_dataframe() (sed.loader.sxp.loader.sxploader method)": [[13, "sed.loader.sxp.loader.SXPLoader.read_dataframe", false]], "read_env_var() (in module sed.core.config)": [[7, "sed.core.config.read_env_var", false]], "remove() (sed.dataset.dataset.dataset 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"save_energy_correction() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.save_energy_correction", false]], "save_energy_offset() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.save_energy_offset", false]], "save_env_var() (in module sed.core.config)": [[7, "sed.core.config.save_env_var", false]], "save_momentum_calibration() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.save_momentum_calibration", false]], "save_splinewarp() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.save_splinewarp", false]], "save_transformations() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.save_transformations", false]], "save_workflow_params() (sed.core.sedprocessor method)": [[8, "sed.core.SedProcessor.save_workflow_params", false]], "sed.binning": [[5, "module-sed.binning", false]], "sed.binning.numba_bin": [[5, "module-sed.binning.numba_bin", false]], "sed.binning.utils": [[5, "module-sed.binning.utils", false]], "sed.calibrator.delay": [[6, "module-sed.calibrator.delay", false]], "sed.calibrator.energy": [[6, "module-sed.calibrator.energy", false]], "sed.calibrator.momentum": [[6, "module-sed.calibrator.momentum", false]], "sed.core": [[8, "module-sed.core", false]], "sed.core.config": [[7, "module-sed.core.config", false]], "sed.core.dfops": [[10, "module-sed.core.dfops", false]], "sed.core.metadata": [[14, "module-sed.core.metadata", false]], "sed.dataset.dataset": [[9, "module-sed.dataset.dataset", false]], "sed.diagnostics": [[11, "module-sed.diagnostics", false]], "sed.io": [[12, "module-sed.io", false]], "sed.loader.base.loader": [[13, "module-sed.loader.base.loader", false]], "sed.loader.flash.loader": [[13, "module-sed.loader.flash.loader", false]], "sed.loader.flash.metadata": [[13, "module-sed.loader.flash.metadata", false]], "sed.loader.generic.loader": [[13, "module-sed.loader.generic.loader", false]], "sed.loader.loader_interface": [[13, "module-sed.loader.loader_interface", 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diff --git a/sed/develop/sed/metadata.html b/sed/develop/sed/metadata.html index 076e40f..8d0f00a 100644 --- a/sed/develop/sed/metadata.html +++ b/sed/develop/sed/metadata.html @@ -8,7 +8,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
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diff --git a/sed/develop/tutorial/10_hextof_workflow_trXPS_bam_correction.html b/sed/develop/tutorial/10_hextof_workflow_trXPS_bam_correction.html index 362da1e..84abf1d 100644 --- a/sed/develop/tutorial/10_hextof_workflow_trXPS_bam_correction.html +++ b/sed/develop/tutorial/10_hextof_workflow_trXPS_bam_correction.html @@ -8,7 +8,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
@@ -702,9 +702,9 @@[9]:
fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+
Now we make fit to determine precise t\(_0\) position and cross-correlation using lmfit fit models
As we see the sidebands are quite broad and one of the possible reasons for this could be long or short-term drifts (jitter) of the FEL arrival time with respect to e.g. optical laser or differences in the intra-bunch arrival time. To check and correct for this we can look at beam arrival monitor (BAM). The BAM gives a pulse-resolved measure of the FEL arrival time with respect to a master clock.
@@ -949,14 +949,14 @@As we can see, jitter between FEL and pump laser is quite significant withing a pulse train as well as over the whole measurement period.
[12]:
fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+
fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')
res_bam.sel(bam=slice(-6400,-5100)).sum('trainId').plot(ax=ax[0],robust=True, cmap='terrain')
res_bam.sel(bam=slice(-6400,-5100)).sum('pulseId').plot(ax=ax[1],robust=True, cmap='terrain')
plt.show()
@@ -967,7 +967,7 @@ Check BAM versus pulse and train IDs
-
+
[15]:
fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+
We clearly see an effect of BAM corrections - side bands are visible much nicer and width became smaller.
[18]:
fig,ax=plt.subplots(2,2,figsize=(6,8),layout="constrained")
+
-INFO - Use feature ranges: [(4120.2, 4199.4), (4156.2, 4242.6), (4197.6, 4289.4), (4237.2, 4338.0)].
+INFO - Use feature ranges: [(4120.2, 4199.4), (4156.2, 4242.6), (4195.8, 4289.4), (4237.2, 4338.0)].
INFO - Extracted energy features: [[4.1472e+03 1.0000e+00]
[4.1850e+03 1.0000e+00]
[4.2246e+03 1.0000e+00]
@@ -685,13 +685,13 @@ find calibration parameters
Now that we have the calibration parameters, we can generate the energy axis for each spectrum
[11]:
@@ -796,14 +796,14 @@ Now we can use those parameters and load our trXPS data using the additional
-[<matplotlib.lines.Line2D at 0x7f0d7817b760>]
+[<matplotlib.lines.Line2D at 0x7ffa1814ee00>]
INFO - Adding energy column to dataframe:
-INFO - Using energy calibration parameters generated on 03/02/2025, 19:37:44
+INFO - Using energy calibration parameters generated on 03/03/2025, 15:07:55
INFO - Dask DataFrame Structure:
trainId pulseId electronId dldPosX dldPosY dldTimeSteps pulserSignAdc bam timeStamp monochromatorPhotonEnergy gmdBda delayStage sampleBias tofVoltage extractorVoltage extractorCurrent cryoTemperature sampleTemperature dldTimeBinSize dldSectorID energy
npartitions=14
@@ -1079,7 +1079,7 @@ Append energy axis into a data frame, bin and visualize data in the calibrat
bins = [200,60]
res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time="delayStage")
-fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')
fig.suptitle(f"Run {run_number}: W 4f, side bands")
res_corr.plot(ax=ax[0], cmap='terrain')
ax[0].set_title('raw')
@@ -1093,7 +1093,7 @@ Append energy axis into a data frame, bin and visualize data in the calibrat
-
+
[18]:
@@ -1122,7 +1122,7 @@ Append energy axis into a data frame, bin and visualize data in the calibrat
-
+
[19]:
@@ -1157,14 +1157,14 @@ Compare to reference
-<matplotlib.legend.Legend at 0x7f0d6d796260>
+<matplotlib.legend.Legend at 0x7ffa0db1e6e0>
SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
-CPU times: user 1.09 s, sys: 25.9 ms, total: 1.11 s
-Wall time: 1.11 s
+CPU times: user 1.13 s, sys: 22.1 ms, total: 1.15 s
+Wall time: 1.15 s
-CPU times: user 591 ms, sys: 169 ms, total: 760 ms
-Wall time: 659 ms
+CPU times: user 634 ms, sys: 158 ms, total: 792 ms
+Wall time: 690 ms
-[<matplotlib.lines.Line2D at 0x7f69cf1795a0>]
+[<matplotlib.lines.Line2D at 0x7f604b7bd9c0>]
INFO - Calculated thin spline correction based on the following landmarks:
-pouter_ord: [[203.00123805 342.99464128]
- [299.8734595 346.1974292 ]
- [350.96138189 244.78936744]
- [305.64461269 150.1951346 ]
- [199.36340167 152.83763302]
- [153.40802309 243.06945515]]
-pcent: (249.24662820754756, 249.23950759291188)
+pouter_ord: [[203.00580996 342.98729171]
+ [299.87644574 346.19515379]
+ [350.95005141 244.77542762]
+ [305.64158514 150.20494501]
+ [199.36525176 152.83519414]
+ [153.4003923 243.05030077]]
+pcent: (249.2343791270372, 249.23280967634267)
INFO - Adding kx/ky columns to dataframe:
-INFO - Using momentum calibration parameters generated on 03/02/2025, 19:39:33
+INFO - Using momentum calibration parameters generated on 03/03/2025, 15:09:48
INFO - Dask DataFrame Structure:
X Y t ADC Xm Ym kx ky
npartitions=100
@@ -939,19 +939,19 @@ 1st step:
INFO - Applying energy correction to dataframe...
-INFO - Using energy correction parameters generated on 03/02/2025, 19:39:34
+INFO - Using energy correction parameters generated on 03/03/2025, 15:09:49
INFO - Dask DataFrame Structure:
X Y t ADC Xm Ym kx ky tm
npartitions=100
@@ -1037,13 +1037,13 @@ 1. Step:#
-
+
INFO - Adding energy column to dataframe:
-INFO - Using energy calibration parameters generated on 03/02/2025, 19:39:43
+INFO - Using energy calibration parameters generated on 03/03/2025, 15:09:58
INFO - Dask DataFrame Structure:
X Y t ADC Xm Ym kx ky tm energy
npartitions=100
@@ -1266,68 +1266,68 @@ 4. Delay calibration:
0
- 0.382659
- 0.382659
- 0.382659
- 0.382659
- -11.661874
- 86.884819
- -2.091352
- -1.827012
- -47.805803
- -25.223820
+ -0.259665
+ -0.259665
+ -0.259665
+ -0.259665
+ 0.000000
+ 0.000000
+ -2.060071
+ -2.060071
+ -48.485684
+ -25.223993
1
- 365.315959
- 1002.315959
- 70101.315959
- 6317.315959
- 355.740561
- 1032.431234
- -1.105838
- 0.709306
- 70084.308759
- -9.315628
+ 365.002224
+ 1002.002224
+ 70101.002224
+ 6317.002224
+ 355.428064
+ 1032.223862
+ -1.106676
+ 0.708750
+ 70083.991189
+ -9.315051
2
- 760.595357
- 817.595357
- 75614.595357
- 6315.595357
- 790.976288
- 839.244933
- 0.061631
- 0.191106
- 75613.724423
- -16.716855
+ 761.028231
+ 818.028231
+ 75615.028231
+ 6316.028231
+ 791.431767
+ 839.639005
+ 0.062853
+ 0.192163
+ 75614.147013
+ -16.717267
3
- 692.312996
- 971.312996
- 66455.312996
- 6317.312996
- 713.880148
- 985.322699
- -0.145170
- 0.582943
- 66449.618228
- -0.834153
+ 692.105075
+ 971.105075
+ 66455.105075
+ 6317.105075
+ 713.665236
+ 985.119143
+ -0.145747
+ 0.582397
+ 66449.417851
+ -0.833556
4
- 671.255668
- 712.255668
- 73026.255668
- 6317.255668
- 697.275649
- 741.568628
- -0.189710
- -0.070899
- 73025.872534
- -13.817439
+ 671.053876
+ 712.053876
+ 73026.053876
+ 6317.053876
+ 697.064542
+ 741.394322
+ -0.190276
+ -0.071367
+ 73025.667607
+ -13.817176
@@ -1354,28 +1354,28 @@ 4. Delay calibration:
-<matplotlib.collections.QuadMesh at 0x7f6a1767dbd0>
+<matplotlib.collections.QuadMesh at 0x7f609cf180a0>
[7]:
@@ -656,7 +656,7 @@ Load Data
-INFO - No landmarks defined, using momentum correction parameters generated on 03/02/2025, 19:39:26
+INFO - No landmarks defined, using momentum correction parameters generated on 03/03/2025, 15:09:41
INFO - Calculated thin spline correction based on the following landmarks:
pouter_ord: [[203.2 341.96]
[299.16 345.32]
@@ -671,19 +671,19 @@ Load Data
-
+
[8]:
@@ -748,7 +748,7 @@ Load Data
INFO - Adding kx/ky columns to dataframe:
-INFO - Using momentum calibration parameters generated on 03/02/2025, 19:39:33
+INFO - Using momentum calibration parameters generated on 03/03/2025, 15:09:48
INFO - Dask DataFrame Structure:
X Y t ADC Xm Ym kx ky
npartitions=100
@@ -775,7 +775,7 @@ Load Data
INFO - Applying energy correction to dataframe...
-INFO - Using energy correction parameters generated on 03/02/2025, 19:39:34
+INFO - Using energy correction parameters generated on 03/03/2025, 15:09:49
INFO - Dask DataFrame Structure:
X Y t ADC Xm Ym kx ky tm
npartitions=100
@@ -802,7 +802,7 @@ Load Data
INFO - Adding energy column to dataframe:
-INFO - Using energy calibration parameters generated on 03/02/2025, 19:39:43
+INFO - Using energy calibration parameters generated on 03/03/2025, 15:09:58
INFO - Dask DataFrame Structure:
X Y t ADC Xm Ym kx ky tm energy
npartitions=100
@@ -832,28 +832,28 @@ Load Data
-
+
@@ -590,7 +590,7 @@ Important note1646339970
12
0
- 780.653621
- 689.653621
- 3049.653621
+ 780.810118
+ 689.810118
+ 3049.810118
32914.0
8976.09375
1.679395e+09
@@ -834,9 +834,9 @@ inspect the dataframe1646339970
12
1
- 780.688296
- 690.688296
- 3048.688296
+ 781.170875
+ 691.170875
+ 3049.170875
32914.0
8976.09375
1.679395e+09
@@ -857,9 +857,9 @@ inspect the dataframe1646339970
22
0
- 561.969661
- 230.969661
- 5728.969661
+ 562.322691
+ 231.322691
+ 5729.322691
32914.0
8990.37500
1.679395e+09
@@ -880,9 +880,9 @@ inspect the dataframe1646339970
22
1
- 938.253866
- 947.253866
- 5730.253866
+ 938.103779
+ 947.103779
+ 5730.103779
32914.0
8990.37500
1.679395e+09
@@ -903,9 +903,9 @@ inspect the dataframe1646339970
27
0
- 535.932444
- 853.932444
- 1570.932444
+ 535.856488
+ 853.856488
+ 1570.856488
32914.0
8982.87500
1.679395e+09
@@ -941,7 +941,7 @@ Visualizing event histograms
-
+
[13]:
@@ -1405,14 +1405,14 @@ visualize the result
-<matplotlib.collections.QuadMesh at 0x7f62104c0850>
+<matplotlib.collections.QuadMesh at 0x7f301432fa30>
[15]:
fig,ax = plt.subplots(1,3,figsize=(6,4), layout='tight')
-res_chessy.plot(ax=ax[0], robust=True)
-res_t05.plot(ax=ax[1], robust=True)
-res_t10.plot(ax=ax[2], robust=True)
+fig,ax = plt.subplots(1,3,figsize=(6,2), layout='tight')
+res_chessy.plot(ax=ax[0], robust=True, add_colorbar=False)
+res_t05.plot(ax=ax[1], robust=True, add_colorbar=False)
+res_t10.plot(ax=ax[2], robust=True, add_colorbar=False)
-<matplotlib.collections.QuadMesh at 0x7f62181aed70>
+<matplotlib.collections.QuadMesh at 0x7f301440eb60>
TODO: here we can add the evaluation of the spot size.
We binned not only in dldTime but also in sampleBias. This allows us to separate the spectra obtained at different bias values.
INFO - Adding energy column to dataframe:
-INFO - Using energy calibration parameters generated on 03/02/2025, 19:45:57
+INFO - Using energy calibration parameters generated on 03/03/2025, 15:16:32
INFO - Dask DataFrame Structure:
trainId pulseId electronId dldPosX dldPosY dldTimeSteps pulserSignAdc bam timeStamp monochromatorPhotonEnergy gmdBda delayStage sampleBias tofVoltage extractorVoltage extractorCurrent cryoTemperature sampleTemperature dldTimeBinSize dldSectorID dldTime energy
npartitions=5
@@ -1838,37 +1838,37 @@ generate the energy axis
[39]:
fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')
res.plot(robust=True, ax=ax[0])
bg = res.isel(delayStage=slice(0,10)).mean('delayStage')
(res-bg).plot(robust=True, ax=ax[1])
@@ -2150,14 +2150,14 @@ plot the delayStage values
-<matplotlib.collections.QuadMesh at 0x7f61f40adc00>
+<matplotlib.collections.QuadMesh at 0x7f301415d900>
-
+
[43]:
fig,ax = plt.subplots(1,2,figsize=(6,4))
+
You may note some intensity variation along the delay axis. This comes mainly from inhomogeneous speed of the delay stage, and thus inequivalent amounts of time spent on every delay point. This can be corrected for by normalizing the data to the acquisition time per delay point:
res = sp.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time="delayStage")
-fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')
res.plot(robust=True, ax=ax[0])
bg = res.sel(delayStage=slice(-1,-.2)).mean('delayStage')
(res-bg).plot(robust=True, ax=ax[1])
@@ -2455,7 +2455,7 @@ bin in the corrected delay axis
[44]:
@@ -2477,14 +2477,14 @@ bin in the corrected delay axis
-<matplotlib.collections.QuadMesh at 0x7f61e01b25c0>
+<matplotlib.collections.QuadMesh at 0x7f2fe80c47c0>
[50]:
fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')
res.plot(robust=True, ax=ax[0])
bg = res.sel(delayStage=slice(-1,-.2)).mean('delayStage')
(res-bg).plot(robust=True, ax=ax[1])
@@ -2688,14 +2688,14 @@ Compute the results
-<matplotlib.collections.QuadMesh at 0x7f61e13d6620>
+<matplotlib.collections.QuadMesh at 0x7f2fd43f0340>
-
+
SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
We can also inspect the counts per train as function of the trainId and the pulseId, which gives us a good idea about the evolution of the count rate over the run(s)
[11]:
@@ -769,14 +769,14 @@ PulseIds, ElectronIds
-<matplotlib.collections.QuadMesh at 0x7f0a980a02b0>
+<matplotlib.collections.QuadMesh at 0x7f565e116590>
[12]:
@@ -808,14 +808,14 @@ Spectrum vs. MicrobunchId
-<matplotlib.collections.QuadMesh at 0x7f0a8cfd7ca0>
+<matplotlib.collections.QuadMesh at 0x7f565ff43d60>
We see that the background below the Au 4f core levels slightly changes with microbunch ID. The origin of this is not quite clear yet.
-<matplotlib.legend.Legend at 0x7f0a8cba5c90>
+<matplotlib.legend.Legend at 0x7f56865a6d70>
[23]:
@@ -1329,14 +1329,14 @@ Bin data with energy axis
-<matplotlib.collections.QuadMesh at 0x7f0a8c2c46a0>
+<matplotlib.collections.QuadMesh at 0x7f564bf5abc0>
[26]:
@@ -1418,14 +1418,14 @@ Correct delay stage offset.
-[<matplotlib.lines.Line2D at 0x7f0a80100400>]
+[<matplotlib.lines.Line2D at 0x7f564bf3e830>]
[12]:
@@ -866,7 +866,7 @@ Load Data
INFO - Adding energy column to dataframe:
-INFO - Using energy calibration parameters generated on 03/02/2025, 19:55:25
+INFO - Using energy calibration parameters generated on 03/03/2025, 15:26:23
INFO - Dask DataFrame Structure:
X Y t ADC timeStamps sampleBias Xm Ym kx ky tm energy
npartitions=97
@@ -917,7 +917,7 @@ Load Data
-
+
-<matplotlib.collections.QuadMesh at 0x7f6bdf736a70>
+<matplotlib.collections.QuadMesh at 0x7f74c8cfacb0>
[18]:
@@ -1018,14 +1018,14 @@ Some visualization:
-[<matplotlib.lines.Line2D at 0x7f6bdf414940>]
+[<matplotlib.lines.Line2D at 0x7f74c89fdde0>]
[19]:
@@ -1055,14 +1055,14 @@ Some visualization:
-<matplotlib.collections.QuadMesh at 0x7f6bdf4a3d90>
+<matplotlib.collections.QuadMesh at 0x7f74c897fb20>
[21]:
@@ -1080,14 +1080,14 @@ Some visualization:
-[<matplotlib.lines.Line2D at 0x7f6bdf18ebc0>]
+[<matplotlib.lines.Line2D at 0x7f74c8793370>]
[10]:
@@ -751,7 +751,7 @@ Momentum calibration with orthorhombic axes
INFO - Adding kx/ky columns to dataframe:
-INFO - Using momentum calibration parameters generated on 03/02/2025, 20:00:55
+INFO - Using momentum calibration parameters generated on 03/03/2025, 15:32:08
INFO - Dask DataFrame Structure:
X Y t ADC timeStamps Xm Ym kx ky
npartitions=100
@@ -783,7 +783,7 @@ Bin the top of the valence band
-
+
[11]:
@@ -791,14 +791,14 @@ Bin the top of the valence band
-<matplotlib.collections.QuadMesh at 0x7f546bba4d00>
+<matplotlib.collections.QuadMesh at 0x7f90102d1660>
[5]:
@@ -612,14 +612,14 @@ Load Data
-[<matplotlib.lines.Line2D at 0x7f3d73e4a530>]
+[<matplotlib.lines.Line2D at 0x7f473903ca90>]
We notice some oscillation ontop of the data. These are re-binning artifacts, originating from a non-integer number of machine-bins per bin, as we can verify by binning with a different number of steps:
[6]:
@@ -649,14 +649,14 @@ Load Data
-<matplotlib.legend.Legend at 0x7f3d73ce5ae0>
+<matplotlib.legend.Legend at 0x7f4738f9cdc0>
If we have a very detailed look, with step-sizes smaller than one, we see the digital nature of the original data behind this issue:
[7]:
@@ -684,14 +684,14 @@ Load Data
-[<matplotlib.lines.Line2D at 0x7f3d73bcba60>]
+[<matplotlib.lines.Line2D at 0x7f4738faee00>]
To mitigate this problem, we can add some randomness to the data, and re-distribute events into the gaps in-between bins. This is also termed dithering and e.g. known from image manipulation. The important factor is to add the right amount and right type of random distribution, to end up at a quasi-continuous uniform distribution, but not lose information.
We can use the add_jitter function for this. We can pass it the columns to add jitter to, and the amplitude of a uniform jitter. Importantly, this step should be taken in the very beginning as first step before any dataframe operations are added.
@@ -756,35 +756,35 @@[10]:
@@ -818,14 +818,14 @@ Load Data
-<matplotlib.legend.Legend at 0x7f3d73bcace0>
+<matplotlib.legend.Legend at 0x7f4738d088e0>
This is clearly not enough jitter to close the gaps. The ideal (and default) amplitude is 0.5, which exactly fills the gaps:
[12]:
@@ -873,14 +873,14 @@ Load Data
-<matplotlib.legend.Legend at 0x7f3d73c87940>
+<matplotlib.legend.Legend at 0x7f4738ee2d70>
This jittering fills the gaps, and produces a continuous uniform distribution. Let’s check again the longer-range binning that gave us the oscillations initially:
[13]:
@@ -910,14 +910,14 @@ Load Data
-<matplotlib.legend.Legend at 0x7f3d715f2c20>
+<matplotlib.legend.Legend at 0x7f47409b2a70>
Now, the artifacts are absent, and similarly will they be in any dataframe columns derived from a column jittered in such a way. Note that this only applies to data present in digital (i.e. machine-binned) format, and not to data that are intrinsically continuous.
Also note that too large or not well-aligned jittering amplitudes will
@@ -961,7 +961,7 @@[15]:
@@ -969,14 +969,14 @@ Load Data
-<matplotlib.legend.Legend at 0x7f3d7b5ca860>
+<matplotlib.legend.Legend at 0x7f4738fc7ca0>
If the step-size of digitization is different from 1, the corresponding stepsize (half the distance between digitized values) can be adjusted as shown above.
Also, alternatively also normally distributed noise can be added, which is less sensitive to the exact right amplitude, but will lead to mixing of neighboring voxels, and thus loss of resolution. Also, normally distributed noise is substantially more computation-intensive to generate. It can nevertheless be helpful in situations where e.g. the stepsize is non-uniform.
@@ -1016,7 +1016,7 @@[17]:
@@ -1024,14 +1024,14 @@ Load Data
-<matplotlib.legend.Legend at 0x7f3d75915fc0>
+<matplotlib.legend.Legend at 0x7f4738faf460>
[12]:
fig,ax = plt.subplots(1,2,figsize=(6,4), layout='constrained')
+
[14]:
@@ -979,7 +979,7 @@ XPD from W4f core levelplt.show()
## XPD plots
-fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')
+fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')
res_kx_ky.sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')
ax[0,0].set_title("XPD of $1^{st}$ order sidebands")
res_kx_ky.sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')
@@ -995,7 +995,7 @@ XPD from W4f core level
As we can see there is some structure visible, but it looks very similar to each other. We probably have to do some normalization to remove the detector structure/artefacts. The best option is to divide by a flat-field image. The flat-field image can be obtained from a sample that shows no structure under identical measurement conditions. Unfortunately, we don’t have such a flat-field image.
In this case, we can make a flat-field image from the actual dataset using several different approaches.
@@ -1025,7 +1025,7 @@[16]:
## XPD normalized by background image
-fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')
+fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')
(res_kx_ky/bgd).sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')
(res_kx_ky/bgd).sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')
(res_kx_ky/bgd).sel(energy=slice(-33.6,-33.4)).mean('energy').plot(robust=True, ax=ax[1,0], cmap='terrain')
@@ -1053,7 +1053,7 @@ XPD from W4f core levelfig.suptitle(f'Run {run_number}: XPD patterns after background normalization',fontsize='18')
## XPD normalized by Gaussian-blurred background image
-fig,ax = plt.subplots(2,2,figsize=(6,8), layout='constrained')
+fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')
(res_kx_ky/bgd_blur).sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')
(res_kx_ky/bgd_blur).sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')
(res_kx_ky/bgd_blur).sel(energy=slice(-33.6,-33.4)).mean('energy').plot(robust=True, ax=ax[1,0], cmap='terrain')
@@ -1061,7 +1061,7 @@ XPD from W4f core levelfig.suptitle(f'Run {run_number}: XPD patterns after Gaussian-blurred background normalization',fontsize='18')
## XPD normalized by Gaussian-blurred background image and blurred to improve contrast
-fig,ax = plt.subplots(2,2,figsize=(9,7), layout='constrained')
+fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')
(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-30.3,-29.9)).mean('energy').plot(robust=True, ax=ax[0,0], cmap='terrain')
(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-31.4,-31.2)).mean('energy').plot(robust=True, ax=ax[0,1], cmap='terrain')
(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-33.6,-33.4)).mean('energy').plot(robust=True, ax=ax[1,0], cmap='terrain')
@@ -1083,19 +1083,19 @@ XPD from W4f core level
Sometimes, after this division, you may not be happy with intensity distribution. Thus, other option for background correction is to duplicate the XPD pattern, apply large Gaussian blurring that eliminates the fine structures in the XPD pattern. Then divide the XPD pattern by its blurred version. This process sometimes enhances the visibility of the fine structures a lot.
Third option for background normalization is to use the simultaneously acquired pre-core level region. As an example for W4f 7/2 peak, we define a region on the high energy side of it and integrate in energy to use as a background
SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/develop/workflows/index.html b/sed/develop/workflows/index.html index e22f0a9..7f2862e 100644 --- a/sed/develop/workflows/index.html +++ b/sed/develop/workflows/index.html @@ -9,7 +9,7 @@ -SED 1.0.0a1.dev14+g568085b documentation
+SED 1.0.0a1.dev15+gb3e949f documentation
diff --git a/sed/switcher.json b/sed/switcher.json index a0bdf55..4135ce5 100644 --- a/sed/switcher.json +++ b/sed/switcher.json @@ -12,7 +12,7 @@ }, { "name": "develop", - "version": "1.0.0a1.dev14+g568085b", + "version": "1.0.0a1.dev15+gb3e949f", "url": "https://opencompes.github.io/docs/sed/develop" }, {