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Add WFC3 notebook 'IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb' #106

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merged 12 commits into from
Dec 11, 2023
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Add WFC3 notebook 'IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb' #106

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8055963
updated _toc.yml and _config.yml files
dulude Oct 6, 2023
c6863be
ima_visualization_and_differencing.py: added trailing line
dulude Oct 6, 2023
ce3b1d0
IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipyn…
dulude Oct 6, 2023
fec91ec
PEP8 corrections and removing unecessary imports, pinnin working code…
annierose3 Nov 8, 2023
c694b61
Merge branch 'add_wfc3_ir_ima_visualization_notebook' into transfer-i…
annierose3 Nov 8, 2023
353f6ba
Merge pull request #124 from annierose3/transfer-ir-ima-vis
FDauphin Nov 8, 2023
fc9d3c7
a few more PEP8 corrections, removing Python version from requirement…
annierose3 Nov 13, 2023
95bd85b
Merge pull request #131 from annierose3/transfer-ir-ima-vis
annierose3 Nov 13, 2023
f54e3e4
Reccomended changes after notebook review.
annierose3 Dec 11, 2023
038a4d4
Merge pull request #157 from annierose3/transfer-ir-ima-vis
annierose3 Dec 11, 2023
1bc2ebf
Fix style error
haticekaratay Dec 11, 2023
334db43
Merge branch 'main' into add_wfc3_ir_ima_visualization_notebook
haticekaratay Dec 11, 2023
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1 change: 0 additions & 1 deletion _config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,6 @@ exclude_patterns: [notebooks/DrizzlePac/align_mosaics/align_mosaics.ipynb,
notebooks/WFC3/filter_transformations/filter_transformations.ipynb,
notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb,
notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb,
notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb,
notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb,
notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb,
notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb,
Expand Down
2 changes: 1 addition & 1 deletion _toc.yml
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Expand Up @@ -66,7 +66,7 @@ parts:
# - file: notebooks/WFC3/filter_transformations/filter_transformations.ipynb
# - file: notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
# - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
# - file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
- file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
# - file: notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb
# - file: notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb
# - file: notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb
Expand Down
198 changes: 111 additions & 87 deletions ..._ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
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Expand Up @@ -96,7 +96,6 @@
"- *matplotlib.pyplot* for plotting data\n",
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"- *astropy.io fits* for accessing FITS files\n",
"- *astroquery* for downlaoding data from MAST\n",
"- *ginga* for scaling using zscale\n",
"\n",
"We import the following module:\n",
"- *ima_visualization_and_differencing* to take the difference between reads, plot the ramp, and to visualize the difference in images\n"
Expand All @@ -109,15 +108,10 @@
"outputs": [],
"source": [
"import os\n",
"\n",
"import numpy as np\n",
"from matplotlib import pyplot as plt\n",
"import matplotlib.patheffects as path_effects\n",
"\n",
"from astropy.io import fits\n",
"from astroquery.mast import Observations\n",
"from ginga.util.zscale import zscale\n",
"\n",
"import ima_visualization_and_differencing as diff\n",
"\n",
"%matplotlib inline"
Expand Down Expand Up @@ -162,9 +156,9 @@
"metadata": {},
"outputs": [],
"source": [
"EX_OBS = Observations.query_criteria(obs_id = 'ICQTBB020')\n",
"EX_OBS = Observations.query_criteria(obs_id='ICQTBB020')\n",
"EXOBS_Prods = Observations.get_product_list(EX_OBS)\n",
"yourProd = Observations.filter_products(EXOBS_Prods, obs_id = ['icqtbbbxq', 'icqtbbc0q'], extension = [\"_ima.fits\",\"_flt.fits\"])"
"yourProd = Observations.filter_products(EXOBS_Prods, obs_id=['icqtbbbxq', 'icqtbbc0q'], extension=[\"_ima.fits\", \"_flt.fits\"])"
]
},
{
Expand All @@ -182,7 +176,7 @@
"metadata": {},
"outputs": [],
"source": [
"Observations.download_products(yourProd, mrp_only = False, cache = False)"
"Observations.download_products(yourProd, mrp_only=False, cache=False)"
]
},
{
Expand Down Expand Up @@ -231,7 +225,7 @@
"flt_nominal = 'mastDownload/HST/icqtbbc0q/icqtbbc0q_flt.fits'\n",
"\n",
"image = fits.open(ima_scattered)\n",
"image.info()\n"
"image.info()"
]
},
{
Expand All @@ -258,10 +252,10 @@
"metadata": {},
"outputs": [],
"source": [
"sci16hdr = image['SCI',16].header\n",
"sci16hdr = image['SCI', 16].header\n",
"SAMPNUM_sci16 = sci16hdr['SAMPNUM']\n",
"SAMPTIME_sci16 = sci16hdr['SAMPTIME']\n",
"print(f'For sample number {SAMPNUM_sci16}, the exposure time is {SAMPTIME_sci16}s.')\n"
"print(f'For sample number {SAMPNUM_sci16}, the exposure time is {SAMPTIME_sci16}s.')"
]
},
{
Expand All @@ -270,7 +264,7 @@
"metadata": {},
"outputs": [],
"source": [
"sci1hdr = image['SCI',1].header\n",
"sci1hdr = image['SCI', 1].header\n",
"SAMPNUM_sci1 = sci1hdr['SAMPNUM']\n",
"SAMPTIME_sci1 = sci1hdr['SAMPTIME']\n",
"print(f'For sample number {SAMPNUM_sci1}, the exposure time is {SAMPTIME_sci1:.3f}s.')\n",
Expand Down Expand Up @@ -298,35 +292,37 @@
"metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize = (30, 30))\n",
"fig = plt.figure(figsize=(30, 30))\n",
"fig\n",
"rows = 2\n",
"columns = 2\n",
"\n",
"files = [ima_scattered, flt_scattered, ima_nominal, flt_nominal] \n",
"# If only analyzing one image, please remove the second ima,flt pair from the list \n",
"\n",
"for i,file in enumerate(files):\n",
"for i, file in enumerate(files):\n",
" path, filename = os.path.split(file)\n",
" \n",
"\n",
" image = fits.open(file)\n",
"\n",
" ax = fig.add_subplot(rows, columns, i+1)\n",
" ax.set_title(filename, fontsize = 20)\n",
" \n",
" ax.set_title(filename, fontsize=20)\n",
"\n",
" subplot_titles = ['scattered', 'nominal']\n",
" #Please change the vmin and vmax values to fit your own data\n",
" # Please change the vmin and vmax values to fit your own data\n",
" if i == 0 or i == 1:\n",
" ax.set_title(f'{filename}, {subplot_titles[i//2]}', fontsize = 20)\n",
" im = ax.imshow(image[\"SCI\", 1].data, origin = 'lower',cmap = 'Greys_r', vmin = 0.25, vmax = 1.7)\n",
" ax.set_title(f'{filename}, {subplot_titles[i//2]}', fontsize=20)\n",
" im = ax.imshow(image[\"SCI\", 1].data, origin='lower', \n",
" cmap='Greys_r', vmin=0.25, vmax=1.7)\n",
" else:\n",
" ax.set_title(f'{filename}, {subplot_titles[i//2]}', fontsize = 20)\n",
" im = ax.imshow(image[\"SCI\", 1].data, origin = 'lower',cmap = 'Greys_r', vmin = 0.5, vmax = 1.2)\n",
" plt.colorbar(im, ax = ax)\n",
" ax.set_title(f'{filename}, {subplot_titles[i//2]}', fontsize=20)\n",
" im = ax.imshow(image[\"SCI\", 1].data, origin='lower', \n",
" cmap='Greys_r', vmin=0.5, vmax=1.2)\n",
" plt.colorbar(im, ax=ax)\n",
"\n",
"plt.subplots_adjust(bottom = 0.2, right = 0.5, top = 0.5)\n",
"plt.rc('xtick', labelsize = 10) \n",
"plt.rc('ytick', labelsize = 10) "
"plt.subplots_adjust(bottom=0.2, right=0.5, top=0.5)\n",
"plt.rc('xtick', labelsize=10) \n",
"plt.rc('ytick', labelsize=10) "
]
},
{
Expand Down Expand Up @@ -354,10 +350,10 @@
"outputs": [],
"source": [
"try:\n",
" diff.plot_ima_subplots(ima_filename = ima_scattered, vmin = 0, vmax = 2.2)\n",
" \n",
" diff.plot_ima_subplots(ima_filename=ima_scattered, vmin=0, vmax=2.2)\n",
"\n",
"except FileNotFoundError:\n",
" print(\"No file by this name found\")\n"
" print(\"No file by this name found\")"
]
},
{
Expand All @@ -376,7 +372,7 @@
"outputs": [],
"source": [
"try:\n",
" diff.plot_ima_subplots(ima_filename = ima_nominal, vmin = 0, vmax = 2)\n",
" diff.plot_ima_subplots(ima_filename=ima_nominal, vmin=0, vmax=2)\n",
"\n",
"except FileNotFoundError:\n",
" print(\"No file by this name found\")"
Expand All @@ -395,31 +391,31 @@
"metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize = (10, 8))\n",
"fig = plt.figure(figsize=(10, 8))\n",
"\n",
"ima_files=[ima_scattered, ima_nominal] \n",
"#If only using one image, please remove the extraneous image from this list \n",
"ima_files = [ima_scattered, ima_nominal] \n",
"# If only using one image, please remove the extraneous image from this list \n",
"\n",
"marker_select = ['o','s']\n",
"color_select = ['black','C0']\n",
"marker_select = ['o', 's']\n",
"color_select = ['black', 'C0']\n",
"for i, ima in enumerate(ima_files):\n",
" path, filename = os.path.split(ima)\n",
" \n",
"\n",
" cube, integ_time = diff.read_wfc3(ima)\n",
" median_fullframe = np.nanmedian(cube, axis = (0,1))\n",
" median_fullframe = np.nanmedian(cube, axis=(0, 1))\n",
"\n",
" plt.rcParams.update({'font.size':15})\n",
" plt.rcParams.update({'font.size': 15})\n",
" plt.plot(integ_time[1:], median_fullframe[1:]*integ_time[1:],\n",
" marker = marker_select[i], markersize = 8, color = color_select[i], label = filename)\n",
" marker=marker_select[i], markersize=8, \n",
" color=color_select[i], label=filename)\n",
" plt.legend()\n",
"plt.grid()\n",
"plt.xlabel('Integ. Time (s)', fontsize = 15)\n",
"plt.ylabel('electrons', fontsize = 15)\n",
"plt.rc('xtick', labelsize = 15) \n",
"plt.rc('ytick', labelsize = 15) \n",
"plt.grid(visible = True)\n",
"_=plt.title(\"Comparison of Signal Accumulation Ramp in Nominal vs. Scattered Light Images\", fontsize=15)\n",
" "
"plt.xlabel('Integ. Time (s)', fontsize=15)\n",
"plt.ylabel('electrons', fontsize=15)\n",
"plt.rc('xtick', labelsize=15) \n",
"plt.rc('ytick', labelsize=15) \n",
"plt.grid(visible=True)\n",
"_ = plt.title(\"Comparison of Signal Accumulation Ramp in Nominal vs. Scattered Light Images\", fontsize=15)"
]
},
{
Expand All @@ -441,43 +437,49 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize = (50, 20))\n",
"fig = plt.figure(figsize=(50, 20))\n",
"fig\n",
"rows = 1\n",
"columns = 2\n",
"ima_files = [ima_scattered, ima_nominal] \n",
"#If only using one image, please remove the extraneous image from this list \n",
"# If only using one image, please remove the extraneous image from this list \n",
"\n",
"subplot_titles = ['scattered', 'nominal']\n",
"\n",
"lhs_region = {\"x0\": 50, \"x1\": 250, \"y0\": 100, \"y1\": 900}\n",
"rhs_region = {\"x0\": 700, \"x1\": 900, \"y0\": 100, \"y1\": 900}\n",
"for i, ima in enumerate(ima_files):\n",
"\n",
"lhs_region={\"x0\":50,\"x1\":250,\"y0\":100,\"y1\":900}\n",
"rhs_region={\"x0\":700,\"x1\":900,\"y0\":100,\"y1\":900}\n",
"for i,ima in enumerate(ima_files):\n",
" \n",
" path, filename = os.path.split(ima)\n",
" \n",
"\n",
" cube, integ_time = diff.read_wfc3(ima)\n",
"\n",
" median_fullframe, median_lhs, median_rhs = diff.get_median_fullframe_lhs_rhs(cube, \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)\n",
" \n",
" median_fullframe, median_lhs, median_rhs = diff.get_median_fullframe_lhs_rhs(cube, lhs_region = lhs_region, rhs_region = rhs_region)\n",
" plt.rcParams.update({'font.size':40})\n",
" plt.rcParams.update({'font.size': 40})\n",
" ax = fig.add_subplot(rows, columns, i+1)\n",
" ax.plot(integ_time[1:], median_fullframe[1:]*integ_time[1:], 's', markersize = 25, label = 'Full Frame', color = 'black')\n",
" ax.plot(integ_time[1:], median_lhs[1:]*integ_time[1:], '<', markersize = 20, label = 'LHS', color = 'C1')\n",
" ax.plot(integ_time[1:], median_rhs[1:]*integ_time[1:], '>', markersize = 20, label = 'RHS', color= 'C2')\n",
" ax.set_ylim(0,1800)\n",
" ax.plot(integ_time[1:], median_fullframe[1:]*integ_time[1:], 's', \n",
" markersize=25, label='Full Frame', color='black')\n",
" \n",
" ax.plot(integ_time[1:], median_lhs[1:]*integ_time[1:], '<', \n",
" markersize=20, label='LHS', color='C1')\n",
" \n",
" ax.plot(integ_time[1:], median_rhs[1:]*integ_time[1:], '>', \n",
" markersize=20, label='RHS', color='C2')\n",
" \n",
" ax.set_ylim(0, 1800)\n",
" ax.grid()\n",
" ax.set_xlabel('Integ. Time (s)')\n",
" ax.set_ylabel('electrons')\n",
" ax.legend(loc = 0)\n",
" _=ax.set_title(f'{filename}, {subplot_titles[i]}', fontsize = 40)\n",
" ax.tick_params(axis = \"x\", labelsize = 30) \n",
" ax.tick_params(axis = \"y\", labelsize = 30) "
" ax.legend(loc=0)\n",
" _ = ax.set_title(f'{filename}, {subplot_titles[i]}', fontsize=40)\n",
" ax.tick_params(axis=\"x\", labelsize=30) \n",
" ax.tick_params(axis=\"y\", labelsize=30) "
]
},
{
Expand Down Expand Up @@ -514,10 +516,15 @@
"metadata": {},
"outputs": [],
"source": [
"##If only using one image, please remove the extraneous image from this list \n",
"lhs_region = {\"x0\":50,\"x1\":250,\"y0\":100,\"y1\":900}\n",
"rhs_region = {\"x0\":700,\"x1\":900,\"y0\":100,\"y1\":900}\n",
"diff.plot_ramp_subplots(ima_files = [ima_scattered, ima_nominal], difference_method = 'cumulative', exclude_sources = False, ylims = [-0.3,0.3], lhs_region = lhs_region, rhs_region = rhs_region)"
"# If only using one image, please remove the extraneous image from this list \n",
"lhs_region = {\"x0\": 50, \"x1\": 250, \"y0\": 100, \"y1\": 900}\n",
"rhs_region = {\"x0\": 700, \"x1\": 900, \"y0\": 100, \"y1\": 900}\n",
"diff.plot_ramp_subplots(ima_files=[ima_scattered, ima_nominal], \n",
" difference_method='cumulative', \n",
" exclude_sources=False, \n",
" ylims=[-0.3, 0.3], \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)"
]
},
{
Expand All @@ -540,9 +547,12 @@
"outputs": [],
"source": [
"try:\n",
" lhs_region = {\"x0\":50,\"x1\":250,\"y0\":100,\"y1\":900}\n",
" rhs_region = {\"x0\":700,\"x1\":900,\"y0\":100,\"y1\":900}\n",
" diff.plot_ima_difference_subplots(ima_filename = ima_scattered, difference_method = 'cumulative', lhs_region = lhs_region, rhs_region = rhs_region)\n",
" lhs_region = {\"x0\": 50, \"x1\": 250, \"y0\": 100, \"y1\": 900}\n",
" rhs_region = {\"x0\": 700, \"x1\": 900, \"y0\": 100, \"y1\": 900}\n",
" diff.plot_ima_difference_subplots(ima_filename=ima_scattered, \n",
" difference_method='cumulative', \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)\n",
" \n",
"except FileNotFoundError:\n",
" print(\"No file by this name found\")"
Expand Down Expand Up @@ -570,9 +580,12 @@
"outputs": [],
"source": [
"try:\n",
" lhs_region = {\"x0\":50,\"x1\":250,\"y0\":100,\"y1\":900}\n",
" rhs_region = {\"x0\":700,\"x1\":900,\"y0\":100,\"y1\":900}\n",
" diff.plot_ima_difference_subplots(ima_filename = ima_nominal, difference_method = 'cumulative', lhs_region = lhs_region, rhs_region = rhs_region)\n",
" lhs_region = {\"x0\": 50, \"x1\": 250, \"y0\": 100, \"y1\": 900}\n",
" rhs_region = {\"x0\": 700, \"x1\": 900, \"y0\": 100, \"y1\": 900}\n",
" diff.plot_ima_difference_subplots(ima_filename=ima_nominal, \n",
" difference_method='cumulative', \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)\n",
"\n",
"except FileNotFoundError:\n",
" print(\"No file by this name found\")"
Expand Down Expand Up @@ -609,10 +622,15 @@
"metadata": {},
"outputs": [],
"source": [
"#If only using one image, please remove the extraneous image from this list \n",
"lhs_region = {\"x0\":50,\"x1\":250,\"y0\":100,\"y1\":900}\n",
"rhs_region = {\"x0\":700,\"x1\":900,\"y0\":100,\"y1\":900}\n",
"diff.plot_ramp_subplots(ima_files = [ima_scattered, ima_nominal], difference_method = 'instantaneous', exclude_sources = True, ylims = [0.5,2.5], lhs_region = lhs_region, rhs_region = rhs_region)"
"# If only using one image, please remove the extraneous image from this list \n",
"lhs_region = {\"x0\": 50, \"x1\": 250, \"y0\": 100, \"y1\": 900}\n",
"rhs_region = {\"x0\": 700, \"x1\": 900, \"y0\": 100, \"y1\": 900}\n",
"diff.plot_ramp_subplots(ima_files=[ima_scattered, ima_nominal], \n",
" difference_method='instantaneous', \n",
" exclude_sources=True, \n",
" ylims=[0.5, 2.5], \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)"
]
},
{
Expand All @@ -636,9 +654,12 @@
"outputs": [],
"source": [
"try:\n",
" lhs_region = {\"x0\":50,\"x1\":250,\"y0\":100,\"y1\":900}\n",
" rhs_region = {\"x0\":700,\"x1\":900,\"y0\":100,\"y1\":900}\n",
" diff.plot_ima_difference_subplots(ima_filename = ima_scattered, difference_method = 'instantaneous', lhs_region = lhs_region, rhs_region = rhs_region)\n",
" lhs_region = {\"x0\": 50, \"x1\": 250, \"y0\": 100, \"y1\": 900}\n",
" rhs_region = {\"x0\": 700, \"x1\": 900, \"y0\": 100, \"y1\": 900}\n",
" diff.plot_ima_difference_subplots(ima_filename=ima_scattered, \n",
" difference_method='instantaneous', \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)\n",
"\n",
"except FileNotFoundError:\n",
" print(\"No file by this name found\")"
Expand All @@ -664,7 +685,10 @@
"outputs": [],
"source": [
"try:\n",
" diff.plot_ima_difference_subplots(ima_filename = ima_nominal, difference_method = 'instantaneous', lhs_region = lhs_region, rhs_region = rhs_region)\n",
" diff.plot_ima_difference_subplots(ima_filename=ima_nominal, \n",
" difference_method='instantaneous', \n",
" lhs_region=lhs_region, \n",
" rhs_region=rhs_region)\n",
" \n",
"except FileNotFoundError:\n",
" print(\"No file by this name found\")"
Expand Down Expand Up @@ -770,9 +794,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.0"
"version": "3.8.12"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
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