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Plotting Refactor #242

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5e2ca8b
refactor plotting functions
robelgeda Sep 4, 2025
09d5841
fix subplots params
robelgeda Sep 4, 2025
bf424fc
update plots in docs
robelgeda Sep 4, 2025
8ee3b60
minor plotting fixes
robelgeda Sep 4, 2025
fbe2790
deprecate measure_fwhm
robelgeda Sep 4, 2025
e75b18d
bug fix remove measure_fwhm from all import
robelgeda Sep 5, 2025
42ef6b0
update correction submodule with plotting
robelgeda Sep 7, 2025
e48760f
update docs
robelgeda Sep 7, 2025
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11 changes: 6 additions & 5 deletions docs/correction_grids.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -122,9 +122,7 @@
"source": [
"from matplotlib import pyplot as plt\n",
"\n",
"plt.rcParams['figure.figsize'] = [6, 6]\n",
"plt.rcParams['image.origin'] = 'lower'\n",
"plt.rcParams['font.size'] = 12"
"plt.rcParams.update(pf.PETROFIT_rcParams)"
]
},
{
Expand All @@ -146,7 +144,10 @@
"print(\"PSF Shape = {}\".format(PSF.shape))\n",
"\n",
"# Plot PSF and use vmax and vmin to show difraction spikes\n",
"plt.imshow(PSF, vmin=0, vmax=5e-4)\n",
"pf.imshow(PSF, vmin=0, vmax=5e-4)\n",
"plt.title(\"PSF Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"plt.show()"
]
},
Expand Down Expand Up @@ -460,7 +461,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "main",
"language": "python",
"name": "python3"
},
Expand Down
21 changes: 11 additions & 10 deletions docs/fitting.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -93,22 +93,20 @@
"import numpy as np\n",
"from matplotlib import pyplot as plt\n",
"\n",
"plt.rcParams['figure.figsize'] = [6, 6]\n",
"plt.rcParams['image.origin'] = 'lower'\n",
"plt.rcParams['font.size'] = 12\n",
"plt.rcParams.update(pf.PETROFIT_rcParams)\n",
"\n",
"vmax = 0.005 # Use the image std as max and min of all plots \n",
"vmin = - vmax \n",
"\n",
"fig, axs = plt.subplots(1,2, figsize=[12, 6])\n",
"fig, axs = pf.subplots(1,2)\n",
"plt.sca(axs[0])\n",
"plt.imshow(image.data, vmin=vmin, vmax=vmax)\n",
"pf.imshow(image.data, vmin=vmin, vmax=vmax)\n",
"plt.title(\"Mock Galaxy\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"\n",
"plt.sca(axs[1])\n",
"plt.imshow(rms)\n",
"pf.imshow(rms)\n",
"plt.title(\"RMS Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
Expand Down Expand Up @@ -152,7 +150,10 @@
"print(\"PSF Shape = {}\".format(PSF.shape))\n",
"\n",
"# Plot PSF and use vmax and vmin to show difraction spikes\n",
"plt.imshow(PSF, vmin=0, vmax=PSF.std()/10)\n",
"pf.imshow(PSF, vmin=0, vmax=PSF.std()/10)\n",
"plt.title(\"PSF Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"plt.show()"
]
},
Expand Down Expand Up @@ -504,7 +505,7 @@
"metadata": {},
"outputs": [],
"source": [
"pf.plot_fit(psf_sersic_model, image.data, vmax=vmax, vmin=vmin, figsize=[3*6, 6])\n",
"pf.plot_fit(psf_sersic_model, image.data, vmax=vmax, vmin=vmin)\n",
"plt.show()"
]
},
Expand Down Expand Up @@ -635,14 +636,14 @@
},
"outputs": [],
"source": [
"pf.plot_fit(fitted_model, image.data, vmax=vmax, vmin=vmin, figsize=[3*6, 6])\n",
"pf.plot_fit(fitted_model, image.data, vmax=vmax, vmin=vmin)\n",
"plt.show()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "main",
"language": "python",
"name": "python3"
},
Expand Down
31 changes: 14 additions & 17 deletions docs/fitting_workflow.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -82,22 +82,20 @@
"import numpy as np\n",
"from matplotlib import pyplot as plt\n",
"\n",
"plt.rcParams['figure.figsize'] = [6, 6]\n",
"plt.rcParams['image.origin'] = 'lower'\n",
"plt.rcParams['font.size'] = 12\n",
"plt.rcParams.update(pf.PETROFIT_rcParams)\n",
"\n",
"vmax = 0.05 # Use the image std as max and min of all plots \n",
"vmin = - vmax \n",
"\n",
"fig, axs = plt.subplots(1,2, figsize=[12, 6])\n",
"fig, axs = pf.subplots(1,2)\n",
"plt.sca(axs[0])\n",
"plt.imshow(image.data, vmin=vmin, vmax=vmax)\n",
"pf.imshow(image.data, vmin=vmin, vmax=vmax)\n",
"plt.title(\"Mock Galaxy\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"\n",
"plt.sca(axs[1])\n",
"plt.imshow(rms)\n",
"pf.imshow(rms)\n",
"plt.title(\"RMS Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
Expand Down Expand Up @@ -175,7 +173,6 @@
" npixels=npixels,\n",
" contrast=0.00,\n",
" plot=True, vmax=vmax, vmin=vmin,\n",
" figsize=[12, 6]\n",
")\n",
"\n",
"plt.show()\n",
Expand Down Expand Up @@ -548,7 +545,7 @@
"x_0 = y_0 = cutout_size / 2\n",
"\n",
"# Plot cutout that will be fit \n",
"plt.imshow(fitting_image.data, vmin=vmin, vmax=vmax)\n",
"pf.imshow(fitting_image.data, vmin=vmin, vmax=vmax)\n",
"plt.title(\"Galaxy in Abell 2744\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
Expand Down Expand Up @@ -620,7 +617,10 @@
"print(\"PSF Shape = {}\".format(PSF.shape))\n",
"\n",
"# Plot PSF and use vmax and vmin to show difraction spikes\n",
"plt.imshow(PSF, vmin=0, vmax=PSF.std()/10)\n",
"pf.imshow(PSF, vmin=0, vmax=PSF.std()/10)\n",
"plt.title(\"PSF Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"plt.show()"
]
},
Expand Down Expand Up @@ -754,7 +754,7 @@
"metadata": {},
"outputs": [],
"source": [
"pf.plot_fit(fitted_model, fitting_image_unmasked, vmax=vmax, vmin=vmin, figsize=[3*6, 6])\n",
"pf.plot_fit(fitted_model, fitting_image_unmasked, vmax=vmax, vmin=vmin)\n",
"plt.show()"
]
},
Expand Down Expand Up @@ -879,9 +879,6 @@
" plot=True, vmax=vmax, vmin=vmin, # Show plot with max and min defined above\n",
")\n",
"\n",
"plt.title(\"Model Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"plt.show()"
]
},
Expand Down Expand Up @@ -927,7 +924,7 @@
"\n",
"\n",
"# Plot Image \n",
"plt.imshow(full_fitted_model_image, vmax=vmax, vmin=vmin)\n",
"pf.imshow(full_fitted_model_image, vmax=vmax, vmin=vmin)\n",
"\n",
"model_position = (\n",
" fitted_model_copy.x_0.value,\n",
Expand Down Expand Up @@ -958,8 +955,8 @@
"metadata": {},
"outputs": [],
"source": [
"corrected_p.plot(plot_r=True)\n",
"model_corrected_p.plot(plot_r=True, color='tab:orange')\n",
"ax = corrected_p.plot(plot_r=True)\n",
"model_corrected_p.plot(plot_r=True, color='tab:orange', ax=ax)\n",
"\n",
"plt.gca().get_legend().remove()\n",
"plt.show()"
Expand Down Expand Up @@ -1024,7 +1021,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "main",
"language": "python",
"name": "python3"
},
Expand Down
48 changes: 24 additions & 24 deletions docs/multi_object.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,13 @@
"source": [
"from matplotlib import pyplot as plt\n",
"\n",
"plt.rcParams['figure.figsize'] = [6, 6]\n",
"plt.rcParams['image.origin'] = 'lower'\n",
"plt.rcParams['font.size'] = 12\n",
"plt.rcParams.update(pf.PETROFIT_rcParams)\n",
"\n",
"vmax = 0.01 # Use the image std as max and min of all plots \n",
"vmin = - vmax \n",
"\n",
"plt.imshow(image.data, vmin=vmin, vmax=vmax)\n",
"plt.title(\"Galaxy Group in Abell 2744 Frontier Field\")\n",
"pf.imshow(image.data, vmin=vmin, vmax=vmax)\n",
"plt.title(\"Galaxy Group in\\n Abell 2744 Frontier Field\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"plt.show()"
Expand Down Expand Up @@ -124,7 +122,6 @@
" npixels=npixels,\n",
" contrast=0.00,\n",
" plot=True, vmax=vmax, vmin=vmin,\n",
" figsize=[12, 6]\n",
")\n",
"\n",
"plt.show()\n",
Expand Down Expand Up @@ -281,7 +278,7 @@
"model_list = []\n",
"\n",
"# For each source\n",
"for source in list(petrosian_properties.keys()):\n",
"for counter, source in enumerate(list(petrosian_properties.keys())):\n",
" \n",
" # Get Petrosian\n",
" p = petrosian_properties[source]\n",
Expand Down Expand Up @@ -328,11 +325,10 @@
" model_list.append(sersic_model)\n",
" \n",
" # Over-plot Petrosian radii \n",
" p.imshow(position=position, elong=elong, theta=theta, lw=1.25)\n",
" p.imshow(position=position, elong=elong, theta=theta, lw=1.25, show_legend=counter == 0)\n",
"\n",
"# Plot image of sources \n",
"plt.imshow(image.data, vmax=vmax, vmin=vmin)\n",
"pf.mpl_tick_frame()\n",
"pf.imshow(image.data, vmax=vmax, vmin=vmin)\n",
"plt.xlabel('Pixels')\n",
"plt.ylabel('Pixels')\n",
"\n",
Expand Down Expand Up @@ -385,7 +381,10 @@
"PSF = fits.getdata('data/f105w_psf.fits.gz')\n",
"PSF = PSF / PSF.sum()\n",
"\n",
"plt.imshow(PSF, vmin=0, vmax=PSF.std()/10)"
"pf.imshow(PSF, vmin=0, vmax=PSF.std()/10)\n",
"plt.title(\"PSF Image\")\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")"
]
},
{
Expand Down Expand Up @@ -471,10 +470,10 @@
"# Plot Model Image\n",
"# ----------------\n",
"\n",
"fig, ax = plt.subplots(2, 2, figsize=[12, 12])\n",
"fig, ax = pf.subplots(2, 2, label_gap=0.25)\n",
"\n",
"# Plot raw data\n",
"im = ax[0, 0].imshow(image.data, vmin=vmin, vmax=vmax)\n",
"im = pf.imshow(image.data, vmin=vmin, vmax=vmax, ax=ax[0, 0])\n",
"ax[0, 0].set_title(\"Hubble F105W Image\")\n",
"ax[0, 0].set_xlabel(\"Pixels\")\n",
"ax[0, 0].set_ylabel(\"Pixels\")\n",
Expand All @@ -492,24 +491,24 @@
" ellip = pf.get_source_ellip(source)\n",
" theta = pf.get_source_theta(source)\n",
" \n",
" p.imshow(position=position, elong=elong, theta=theta, lw=1.25)\n",
" p.imshow(position=position, elong=elong, theta=theta, lw=1.25, show_legend=i==0)\n",
" if i == 0:\n",
" plt.legend()\n",
"ax[0, 1].imshow(image.data, vmin=vmin, vmax=vmax)\n",
"pf.imshow(image.data, vmin=vmin, vmax=vmax, ax=ax[0, 1])\n",
"ax[0, 1].set_title(\"Petrosian Radii\")\n",
"ax[0, 1].set_xlabel(\"Pixels\")\n",
"ax[0, 1].set_ylabel(\"Pixels\")\n",
"# ax[0, 1].axis('off')\n",
"\n",
"# Plot Model Image\n",
"ax[1, 0].imshow(fitted_model_image, vmin=vmin, vmax=vmax)\n",
"ax[1, 0].set_title(\"Simultaneously Fitted Sersic Models\")\n",
"pf.imshow(fitted_model_image, vmin=vmin, vmax=vmax, ax=ax[1, 0])\n",
"ax[1, 0].set_title(\"Simultaneously Fitted Models\")\n",
"ax[1, 0].set_xlabel(\"Pixels\")\n",
"ax[1, 0].set_ylabel(\"Pixels\")\n",
"# ax[1, 0].axis('off')\n",
"\n",
"# Plot Residual\n",
"ax[1, 1].imshow(image.data - fitted_model_image, vmin=vmin, vmax=vmax)\n",
"pf.imshow(image.data - fitted_model_image, vmin=vmin, vmax=vmax, ax=ax[1, 1])\n",
"ax[1, 1].set_title(\"Residual\")\n",
"ax[1, 1].set_xlabel(\"Pixels\")\n",
"ax[1, 1].set_ylabel(\"Pixels\")\n",
Expand Down Expand Up @@ -553,22 +552,24 @@
"# Plots\n",
"# -----\n",
"\n",
"fig, axs = plt.subplots(1, 2, figsize=[16, 8])\n",
"fig, axs = pf.subplots(1, 2)\n",
"plt.sca(axs[0])\n",
"plt.imshow(image.data - fitted_model_image, vmin=vmin, vmax=vmax)\n",
"pf.imshow(image.data - fitted_model_image, vmin=vmin, vmax=vmax, ax=axs[0])\n",
"plt.title('Residual Image')\n",
"plt.xlabel(\"Pixels\")\n",
"plt.ylabel(\"Pixels\")\n",
"\n",
"plt.sca(axs[1])\n",
"n, bins, patches = plt.hist(background_image.flatten(), bins=35, align='left', \n",
" color='black', label=\"Binned Residual Image Pixel Values\")\n",
"plt.plot(bins[:-1], n, c='r', linewidth=3)\n",
"plt.axvline(image.data.mean(), label=\"Raw Input Image Mean\", c='g',linestyle=\"--\")\n",
"plt.axvline(noise_mean, label=\"Residual Image Mean\", linestyle=\"--\")\n",
"\n",
"pf.mpl_tick_frame()\n",
"\n",
"plt.xlabel('Flux Bins [{}]'.format(str(image.unit)))\n",
"plt.ylabel('Count')\n",
"plt.title('Residual Image Pixel Value Histogram')\n",
"plt.title('Residual Image\\n Pixel Value Histogram')\n",
"plt.legend()\n",
"\n",
"plt.show()"
Expand Down Expand Up @@ -601,7 +602,6 @@
" npixels=npixels,\n",
" contrast=0.00,\n",
" plot=True, vmax=vmax, vmin=vmin,\n",
" figsize=[12, 6]\n",
")\n",
"\n",
"plt.show()\n",
Expand All @@ -613,7 +613,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "main",
"language": "python",
"name": "python3"
},
Expand Down
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