From ee682afa1fda67635d4bc4398891c322c3b37628 Mon Sep 17 00:00:00 2001 From: mgough-970 Date: Thu, 19 Dec 2024 18:54:29 +0000 Subject: [PATCH] deploy: b2c4c3b56d003282cda3603edf7f98195cdb4ebf --- .../NGC4151_FeII_ContinuumFit.html | 4 ++-- .../JWST_Mstar_dataAnalysis_analysis.html | 10 +++++----- .../01_niriss_wfss_image2_image3.html | 16 ++++++++-------- .../niriss_imaging/niriss-imaging-tutorial.html | 10 +++++----- .../01_niriss_wfss_image2_image3.html | 16 ++++++++-------- .../02_niriss_wfss_spec2.html | 12 ++++++------ .../Imaging_Sky_Background_Estimation.html | 4 ++-- .../rgb_imviz/imviz_rgb_carina.html | 2 +- notebooks/galaxy_redshift/redshift_fitting.html | 8 ++++---- notebooks/ifu_optimal/ifu_optimal.html | 4 ++-- .../MOSspec_advanced.html | 6 +++--- .../niriss_imaging/niriss-imaging-tutorial.html | 10 +++++----- .../Spectral_Extraction.html | 4 ++-- notebooks/rgb_imviz/imviz_rgb_carina.html | 2 +- ...pecviz_notebook_gui_interaction_redshift.html | 6 +++--- 15 files changed, 57 insertions(+), 57 deletions(-) diff --git a/notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.html b/notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.html index 323250624..830b2056a 100644 --- a/notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.html +++ b/notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.html @@ -707,7 +707,7 @@

Video:
- +
@@ -1102,7 +1102,7 @@

Pulling other data - +

Alternative way to do continuum subtraction using numpy#

diff --git a/notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.html b/notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.html index 1700f3bb1..90f2fc047 100644 --- a/notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.html +++ b/notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.html @@ -730,7 +730,7 @@

Read in the SpectrumList (12 unique spectra) - +

Load in the spectrum list from above. Note, only the first spectrum in your list is displayed automatically. You will need to turn on the remaining spectra in the “DATA” drop-down, then hit the “Home” button in the toolbar, and scale our plot accordingly to see the other spectra.#

@@ -779,7 +779,7 @@

Video 2: - +

Developer Note. Need to pick a different unit than meters. https://jira.stsci.edu/browse/JDAT-1792#

@@ -894,7 +894,7 @@

Visualize for Analysis the Single Spectrum1D Object Created Above from All 1
- +

Developer Note: Cannot currently open a spectrum1d output from cubeviz in specviz. https://jira.stsci.edu/browse/JDAT-1791#

@@ -1094,7 +1094,7 @@

As an example lets focus on the amorphous silicate 10 micron region.
- +
@@ -1236,7 +1236,7 @@

Video 6: - +

diff --git a/notebooks/NIRISS/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html b/notebooks/NIRISS/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html index 30e481857..e51c66a84 100644 --- a/notebooks/NIRISS/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html +++ b/notebooks/NIRISS/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html @@ -18819,7 +18819,7 @@

Matplotlib - +

The segmentation maps are also a product of the Image3 pipeline, and they are used the help determine the source catalog. Let’s take a look at those to ensure we are happy with what it is defining as a source.

In the segmentation map, each blue blob should correspond to a physical target. There are cases where sources can be blended, in which case the parameters for making the semgentation map and source catalog should be changed. An example of this can be seen below in the observation 004 F200W filter image where two galaxies at ~(1600, 1300) have been blended into one source. This is discussed in more detail below in Custom Imaging Pipeline Run.

@@ -18892,7 +18892,7 @@

Matplotlib - +

@@ -18957,7 +18957,7 @@

ImViz# exp_obj = getattr(self._obj, attr) - +

@@ -20077,7 +20077,7 @@

Inspecting Custom Results - +

The cell below shows similar information using Imviz instead to visualize this.

@@ -20130,7 +20130,7 @@

Inspecting Custom Results
Plotting: default_image3_calibrated/jw02079-o004_t001_niriss_clear-f150w_i2d.fits

- +

Calibrate the remaining images if you are happy with the above results

@@ -23525,7 +23525,7 @@

Inspecting Custom Results - +

@@ -23607,7 +23607,7 @@

Matching Source IDs Across Catalogs - +

@@ -23797,7 +23797,7 @@

Manually Editing the Source Catalog - + Space Telescope Logo diff --git a/notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.html b/notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.html index 48a10ca1d..dd0b70135 100644 --- a/notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.html +++ b/notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.html @@ -681,7 +681,7 @@

Display uncalibrated image - +

Adjust settings for the viewer:

@@ -13404,7 +13404,7 @@

Display rate image - +

@@ -19083,7 +19083,7 @@

Display cal image - +

@@ -21388,7 +21388,7 @@

Display combined image

- +
@@ -21459,7 +21459,7 @@

Mark the extended and point sources on the image - +

diff --git a/notebooks/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html b/notebooks/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html index e36f92954..9e3bbab74 100644 --- a/notebooks/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html +++ b/notebooks/NIRISS_WFSS_advanced/01_niriss_wfss_image2_image3.html @@ -18780,7 +18780,7 @@

Matplotlib - +

The segmentation maps are also a product of the Image3 pipeline, and they are used the help determine the source catalog. Let’s take a look at those to ensure we are happy with what it is defining as a source.

In the segmentation map, each blue blob should correspond to a physical target. There are cases where sources can be blended, in which case the parameters for making the semgentation map and source catalog should be changed. An example of this can be seen below in the observation 004 F200W filter image where two galaxies at ~(1600, 1300) have been blended into one source. This is discussed in more detail below in Custom Imaging Pipeline Run.

@@ -18853,7 +18853,7 @@

Matplotlib - +

@@ -18912,7 +18912,7 @@

ImViz# 
Plotting: default_image3_calibrated/jw02079-o004_t001_niriss_clear-f200w_i2d.fits
- +

@@ -20142,7 +20142,7 @@

Inspecting Custom Results - +

The cell below shows similar information using Imviz instead to visualize this.

@@ -20185,7 +20185,7 @@

Inspecting Custom Results
Plotting: default_image3_calibrated/jw02079-o004_t001_niriss_clear-f150w_i2d.fits

- +

Calibrate the remaining images if you are happy with the above results

@@ -23698,7 +23698,7 @@

Inspecting Custom Results - +

@@ -23780,7 +23780,7 @@

Matching Source IDs Across Catalogs - +

@@ -23969,7 +23969,7 @@

Manually Editing the Source Catalog - + Space Telescope Logo diff --git a/notebooks/NIRISS_WFSS_advanced/02_niriss_wfss_spec2.html b/notebooks/NIRISS_WFSS_advanced/02_niriss_wfss_spec2.html index a9ffceb18..375f785ad 100644 --- a/notebooks/NIRISS_WFSS_advanced/02_niriss_wfss_spec2.html +++ b/notebooks/NIRISS_WFSS_advanced/02_niriss_wfss_spec2.html @@ -5924,7 +5924,7 @@

Find a Source in the Spec2 Data
Text(0.5, 0.98, 'GR150C F200W')
- +

We can then take a look at the extracted spectrum in this box both in the cal file and the x1d file. In the extracted spectrum below you can see the [OII] and H\(\beta\) emission lines from the galaxy.

Note: The upturned edge effects seen in the 1-D spectrum are due to interpolation at the edges of the extraction box for the current flux calibration. This is also part of an ongoing calibration effort.

@@ -5986,7 +5986,7 @@

Find a Source in the Spec2 Data - +

@@ -38711,7 +38711,7 @@

Look at all of the Files for a Single Source
2024-06-07 14:03:10,904 - stpipe - WARNING -
- +

Overplot these files on top of each other to compare. The two grisms will be different line styles to draw attention to any differences that could be due to the calibration, including contamination, and each blocking filter will be a different color.

@@ -38790,7 +38790,7 @@

Look at all of the Files for a Single Source - +

@@ -38820,7 +38820,7 @@

Look at all of the sources for a single file - +

@@ -38903,7 +38903,7 @@

Visualize where the extracted sources are on the dispersed image, and how th
- +

Continue to explore further, including using the spec3 stage of the pipeline!

Space Telescope Logo diff --git a/notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.html b/notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.html index 242f13f8b..80acff8da 100644 --- a/notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.html +++ b/notebooks/background_estimation_imaging/Imaging_Sky_Background_Estimation.html @@ -692,7 +692,7 @@

Create the nasty sky background - +
@@ -759,7 +759,7 @@

Look at it with noise added and then smoothed a bit

- +
diff --git a/notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.html b/notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.html index bced9efe2..783a4ee23 100644 --- a/notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.html +++ b/notebooks/cross_instrument/rgb_imviz/imviz_rgb_carina.html @@ -583,7 +583,7 @@

Download images and load Imviz - +

diff --git a/notebooks/galaxy_redshift/redshift_fitting.html b/notebooks/galaxy_redshift/redshift_fitting.html index 002eba60e..61970fab9 100644 --- a/notebooks/galaxy_redshift/redshift_fitting.html +++ b/notebooks/galaxy_redshift/redshift_fitting.html @@ -670,7 +670,7 @@

“By eye” redshift measurement with Specviz - +
@@ -871,7 +871,7 @@

Clean up the spectrum

- +
@@ -918,7 +918,7 @@

Clean up the spectrum

- +
@@ -996,7 +996,7 @@

Run the cross correlation function - +

Space Telescope Logo

diff --git a/notebooks/ifu_optimal/ifu_optimal.html b/notebooks/ifu_optimal/ifu_optimal.html index b02209360..fcbca268d 100644 --- a/notebooks/ifu_optimal/ifu_optimal.html +++ b/notebooks/ifu_optimal/ifu_optimal.html @@ -652,7 +652,7 @@

2. Read in NIRSpec IFU Cube - +
@@ -1126,7 +1126,7 @@

12. Optimal Extraction using WebbPSF Model - +

The optimally extracted spectrum is less noisy than the aperture extraction and incorporates fewer bad pixels and cosmic ray events. The OIII line profile is different because extended emission is downweighted with respect to the unresolved quasar nucleus.

Space Telescope Logo diff --git a/notebooks/mos_spectroscopy_advanced/MOSspec_advanced.html b/notebooks/mos_spectroscopy_advanced/MOSspec_advanced.html index b11c3ae64..6acfdfae9 100644 --- a/notebooks/mos_spectroscopy_advanced/MOSspec_advanced.html +++ b/notebooks/mos_spectroscopy_advanced/MOSspec_advanced.html @@ -697,7 +697,7 @@

Use Specviz2d to extract a better 1D spectrum - +

Developer note
Is there a way to get out an uncertainty array from the extraction?
@@ -750,7 +750,7 @@

Use Specviz2d to extract a better 1D spectrum - +

There are still some artifacts in the data, but we can select a subset masking the artifacts and get out a spectrum without unwanted spikes. We can do so using the tool to select a subset with the “add” option (in the top bar) to select multiple regions as part of a single subset.

@@ -2413,7 +2413,7 @@

New instance of Specviz with spectrum and template

- +
Space Telescope Logo

Notebook created by Camilla Pacifici (cpacifici@stsci.edu)
diff --git a/notebooks/niriss_imaging/niriss-imaging-tutorial.html b/notebooks/niriss_imaging/niriss-imaging-tutorial.html index a26c6377f..941197712 100644 --- a/notebooks/niriss_imaging/niriss-imaging-tutorial.html +++ b/notebooks/niriss_imaging/niriss-imaging-tutorial.html @@ -674,7 +674,7 @@

Display uncalibrated image - +

Adjust settings for the viewer:

@@ -7487,7 +7487,7 @@

Display rate image - +

@@ -11152,7 +11152,7 @@

Display cal image - +

@@ -13185,7 +13185,7 @@

Display combined image

- +
@@ -13242,7 +13242,7 @@

Mark the extended and point sources on the image - +

Point sources will be marked by small pink circles and extended sources will be marked by larger white circles.

diff --git a/notebooks/optimal_extraction_dynamic/Spectral_Extraction.html b/notebooks/optimal_extraction_dynamic/Spectral_Extraction.html index 9453fdf2e..b71c155ce 100644 --- a/notebooks/optimal_extraction_dynamic/Spectral_Extraction.html +++ b/notebooks/optimal_extraction_dynamic/Spectral_Extraction.html @@ -732,7 +732,7 @@

Define an extraction region ../../_images/d1f371cee6e0751906e55f3198f6efbdee934e8ed5522fa33c5b88351a058cfd.png - +

We get the region coordinates from the bounding rectangle – in this case, setting the coordinates to x1=51, y1=3, x2=1268, y2=9 seems fine – or, we can set them directly. Finally, we create a new array containing only our extraction region (so that we don’t need to continually index our original array).

@@ -842,7 +842,7 @@

Create kernel slice ../../_images/ee74d29e7ee7d0c2e680b8cc559df7fdfe7210b2c79b581bb3ff9179b52f9066.png - +

A column index of 670 and width 50 seem to work reasonably well for this file, so we can now generate the final slice for kernel fitting.

diff --git a/notebooks/rgb_imviz/imviz_rgb_carina.html b/notebooks/rgb_imviz/imviz_rgb_carina.html index 03629fec6..e1c57f18a 100644 --- a/notebooks/rgb_imviz/imviz_rgb_carina.html +++ b/notebooks/rgb_imviz/imviz_rgb_carina.html @@ -550,7 +550,7 @@

RGB images with Imviz

- +

WCS Linking Controls#

diff --git a/notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.html b/notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.html index bad16088e..d636e7e83 100644 --- a/notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.html +++ b/notebooks/specviz_notebookGUI_interaction/specviz_notebook_gui_interaction_redshift.html @@ -699,7 +699,7 @@

2. Open Specviz and load the 1D spectra we are interested in - +

The following cell opens one extension of the x1d file (75), creates a Spectrum1D object, and loads it into Specviz. A mask is set to only keep the part of the spectra with good sensitivity (1.34 to 1.66 micron) in the F150W filter.

@@ -843,7 +843,7 @@

4. Use the redshift slider in Specviz to find the redshift - +

I load just the interesting spectrum (spec1d_line).

@@ -911,7 +911,7 @@

5. Model the continuum of the spectrum - +