fix aspect ratios

Author: rettigl

tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb

@@ -238,7 +238,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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",
@@ -523,7 +523,7 @@
     "plt.legend(loc=1)\n",
     "plt.title(\"Sidebands with bam correction\")\n",
     "\n",
-    "fig.suptitle(f'Run {run_number}: Effect of BAM correction',fontsize='22')"
+    "fig.suptitle(f'Run {run_number}: Effect of BAM correction',fontsize='14')"
    ]
   },
   {
@@ -545,7 +545,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "sed-processor-7Jy-bAA8-py3.9",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -559,7 +559,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb

@@ -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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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",

tutorial/1_binning_fake_data.ipynb

@@ -106,7 +106,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, axs = plt.subplots(1, 3, figsize=(8, 2.5), constrained_layout=True)\n",
+    "fig, axs = plt.subplots(1, 3, figsize=(6, 1.875), constrained_layout=True)\n",
     "for i in range(3):\n",
     "    axs[i].imshow(res.sum(i))"
    ]
@@ -164,7 +164,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, axs = plt.subplots(1, 3, figsize=(8, 2.5), constrained_layout=True)\n",
+    "fig, axs = plt.subplots(1, 3, figsize=(6, 1.875), constrained_layout=True)\n",
     "for dim, ax in zip(binAxes, axs):\n",
     "    res.sum(dim).plot(ax=ax)"
    ]
@@ -179,11 +179,8 @@
   }
  ],
  "metadata": {
-  "interpreter": {
-   "hash": "728003ee06929e5fa5ff815d1b96bf487266025e4b7440930c6bf4536d02d243"
-  },
   "kernelspec": {
-   "display_name": "python3",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -197,7 +194,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,

tutorial/4_hextof_workflow.ipynb

@@ -759,7 +759,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=2.25), 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=(6,3))\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25))\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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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])"
@@ -1017,7 +1017,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "python3",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -1031,7 +1031,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

tutorial/9_hextof_workflow_trXPD.ipynb

@@ -291,7 +291,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig,ax = plt.subplots(1,2,figsize=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.25), 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=(6,6), layout='constrained')\n",
+    "fig,ax = plt.subplots(2,2,figsize=(6,4.7), 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=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.7), 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",
@@ -397,28 +397,28 @@
    "outputs": [],
    "source": [
     "## XPD normalized by background image\n",
-    "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n",
+    "fig,ax = plt.subplots(2,2,figsize=(6,4.7), 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",
     "(res_kx_ky/bgd).sel(energy=slice(-37.0,-36.0)).mean('energy').plot(robust=True, ax=ax[1,1], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: XPD patterns after background normalization',fontsize='14')\n",
+    "fig.suptitle(f'Run {run_number}: XPD patterns after background normalization',fontsize='11')\n",
     "\n",
     "## XPD normalized by Gaussian-blurred background image\n",
-    "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n",
+    "fig,ax = plt.subplots(2,2,figsize=(6,4.7), 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",
     "(res_kx_ky/bgd_blur).sel(energy=slice(-37.0,-36.0)).mean('energy').plot(robust=True, ax=ax[1,1], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: XPD patterns after Gaussian-blurred background normalization',fontsize='14')\n",
+    "fig.suptitle(f'Run {run_number}: XPD patterns after Gaussian-blurred background normalization',fontsize='11')\n",
     "\n",
     "## XPD normalized by Gaussian-blurred background image and blurred to improve contrast\n",
-    "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n",
+    "fig,ax = plt.subplots(2,2,figsize=(6,4.7), 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",
     "(xr.apply_ufunc(gaussian_filter, res_kx_ky/bgd_blur, 1)).sel(energy=slice(-37.0,-36.0)).mean('energy').plot(robust=True, ax=ax[1,1], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: resulting Gaussian-blurred XPD patterns',fontsize='14')"
+    "fig.suptitle(f'Run {run_number}: resulting Gaussian-blurred XPD patterns',fontsize='11')"
    ]
   },
   {
@@ -451,12 +451,12 @@
     "W_5p_blur = xr.apply_ufunc(gaussian_filter, W_5p, 15)\n",
     "\n",
     "### Visualize results\n",
-    "fig,ax = plt.subplots(2,2,figsize=(6,6), layout='constrained')\n",
+    "fig,ax = plt.subplots(2,2,figsize=(6,4.7), 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",
     "(W_5p/W_5p_blur).plot(robust=True, ax=ax[1,1], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: XPD patterns after Gaussian Blur normalization',fontsize='14')\n",
+    "fig.suptitle(f'Run {run_number}: XPD patterns after Gaussian Blur normalization',fontsize='11')\n",
     "\n",
     "### Apply Gaussian Blur to resulted images to improve contrast\n",
     "SB_norm = xr.apply_ufunc(gaussian_filter, SB/SB_blur, 1)\n",
@@ -465,12 +465,12 @@
     "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=(6,6), layout='constrained')\n",
+    "fig,ax = plt.subplots(2,2,figsize=(6,4.7), 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",
     "W_5p_norm.plot(robust=True, ax=ax[1,1], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: XPD patterns after Gauss Blur normalization',fontsize='14')                   "
+    "fig.suptitle(f'Run {run_number}: XPD patterns after Gauss Blur normalization',fontsize='11')                   "
    ]
   },
   {
@@ -503,15 +503,15 @@
     "W_4f_7_nrm2_blur = xr.apply_ufunc(gaussian_filter, W_4f_7_nrm2, 1)\n",
     "\n",
     "### Visualize all steps\n",
-    "fig,ax = plt.subplots(4,2,figsize=(6,12), layout='constrained')\n",
+    "fig,ax = plt.subplots(4,2,figsize=(6,8), layout='constrained')\n",
     "W_4f_7.plot(robust=True, ax=ax[0,0], cmap='terrain')\n",
     "W_4f_7_bgd.plot(robust=True, ax=ax[0,1], cmap='terrain')\n",
     "W_4f_7_nrm1.plot(robust=True, ax=ax[1,0], cmap='terrain')\n",
     "W_4f_7_nrm1_blur.plot(robust=True, ax=ax[1,1], cmap='terrain')\n",
     "W_4f_7_bgd_blur.plot(robust=True, ax=ax[2,0], cmap='terrain')\n",
     "W_4f_7_nrm2.plot(robust=True, ax=ax[2,1], cmap='terrain')\n",
     "W_4f_7_nrm2_blur.plot(robust=True, ax=ax[3,0], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: XPD patterns of W4f7/2 with pre-core level normalization',fontsize='14')  "
+    "fig.suptitle(f'Run {run_number}: XPD patterns of W4f7/2 with pre-core level normalization',fontsize='11')  "
    ]
   },
   {
@@ -521,11 +521,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig,ax = plt.subplots(1,3,figsize=(6,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,3,figsize=(6,2), layout='constrained')\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], cmap='terrain')\n",
     "W_4f_7_norm.plot(robust=True, ax=ax[1], cmap='terrain')\n",
     "W_4f_7_nrm2_blur.plot(robust=True, ax=ax[2], cmap='terrain')\n",
-    "fig.suptitle(f'Run {run_number}: comparison of different normalizations\\nof XPD pattern for W4f 7/2 peak with Gaussian Blur',fontsize='14')"
+    "fig.suptitle(f'Run {run_number}: comparison of different normalizations\\nof XPD pattern for W4f 7/2 peak with Gaussian Blur',fontsize='11')"
    ]
   },
   {
@@ -539,7 +539,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "python3",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -553,7 +553,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,