Getting Started#

The Data Inspector#

For precise pixel-level analysis, you can open the Data Inspector.

1. Right-click on any point in the spectrum plot.

2. Select Inspect Data (near …) from the context menu.

TThis opens a floating window displaying the raw values centered on the pixel you clicked. The table headers use scientific notation for clarity:

• λ: Central wavelength of the pixel.

• λmin / λmax: The lower and upper boundaries of the pixel bin.

• F: Flux density.

• dF: 1-sigma error estimate.

• Other columns, containing the continuum and additional information, when present (such as the resolution column resol, mentioned below).

The table supports infinite scrolling, automatically loading more data as you move up or down.

Toggles#

You can show or hide specific layers of the plot:

• 1-sigma error: Hides the grey error shading.

• Show error as line: Instead of a shaded band, plots the error array (\(dy\)) as a separate line. Useful for inspecting noise structure in high-resolution spectra.

• Normalization: Hides the continuum level (dashed black line).

• Absorption model: Hides the Voigt profile fits (solid red line).

• Systems: Hides the vertical tick marks indicating identified systems.

• Aux. Column: Select an additional data column (e.g., abs_mask, running_std) to overlay on the plot.

• Strong emission lines: Shows markers for major emission lines (e.g., Ly-\(\alpha\), CIV).

  Note

  This requires defining the emission redshift first (see Setting Session Properties).

• Show Iso-Mag Grid: Overlays curves of constant AB magnitude.

  Note

  This requires flux calibration (see Flux Calibration).

Axis Controls#

• Units: You can switch the X-axis display between nm, Angstrom, and micron on the fly.

• Normalize F: Plots the flux relative to the continuum (showing \(f = F / F_\mathrm{cont}\)) (this control becomes active only when a cont column is present).

• Show SNR: Plots the Signal-to-Noise Ratio instead of flux.

  • Error Col.: When showing SNR, you can select which column to use as the noise estimate (default is dF).

• Logarithmic \(\lambda\): Switches the X-axis to a logarithmic scale.

Axis Limits#

You can manually set the precise bounds of the plot view. Enter values for \(\lambda\) Min/Max and F Min/Max and press Enter to apply them. These boxes automatically update when you zoom or pan interactively.

The Redshift Cursor#

This is a handy tool for quick visual inspection.

1. In the Redshift Cursor section, enter a transition name (e.g., Ly_a, CIV, MgII) and a redshift z.

2. Check the Show Cursor Lines box.

3. Vertical dashed lines will appear on the plot indicating where that transition should be found. You can update the z value to slide the cursor along the spectrum.

Interactive Setting: You can Right-click directly on the plot background to open a context menu. Select Set emission redshift to z=… to instantly update the session’s \(z_{em}\) based on the cursor’s current position.

The Continuum Editor#

Located at the bottom of the sidebar, this panel allows you to interactively refine the continuum shape using spline knots. See the Interactive Manual Editing in the Continuum Fitting tutorial for a detailed guide on using the slider, spacing box, and editing tools.

Switching Sessions#

If you loaded multiple spectra, click on their names in this list to switch the main view instantly.

Visualizing Multiple Spectra (Ghost Overlay)#

You can easily compare multiple spectra simultaneously directly in the main plot window:

• How to use: Hold Ctrl (or Cmd on macOS) and click on multiple sessions in the left-hand Session List. You can also use Shift+Click to select a continuous range.

• What you’ll see: Your primary active session remains fully featured (showing models, continuums, and system markers). The additional selected sessions will appear underneath as “ghost” spectra, plotted in distinct, colorblind-friendly colors with semi-transparent flux and error bands. A legend will automatically appear to help you identify them.

• Smart Scaling: The ghost spectra are fully integrated with your View Controls! If you toggle Normalize F, all visible spectra will automatically rescale to match the active view.

Session Info & Properties#

Right-click on any session in the list to open the context menu. This menu offers several powerful tools:

• View Info: Opens the Session Inspector. Here you can see (and edit) critical metadata:

  • Object Name

  • Emission Redshift (\(z_\mathrm{em}\)): Crucial for many recipes like the Ly-\(\alpha\) forest analysis.

  • Resolution (\(R\)): Essential for accurate Voigt profile fitting.

  Note

  Setting a global resolution here will automatically generate a pixel-by-pixel resol column across your entire spectrum, which you can verify in the Data Inspector.

• Duplicate: Creates a complete copy of the current session. This allows you to branch your analysis (e.g., to test two different continuum fits on the same data).

The Log Scripter#

Astrocook automatically records every operation you perform (smoothing, fitting, editing). Right-click a session and select View Log to open the Log Scripter.

This dialog allows you to:

• Review History: See a readable list of every recipe run on this session.

• Undo/Redo: Step back through your analysis history.

  Tip

  You can access Undo/Redo also from the Edit menu (see Editing Data) or using the standard key combinations Ctrl+Z/Ctrl+Y (Cmd+Z/Cmd+Shift+Z on Mac).

• Run All: Re-run the entire analysis pipeline from the original raw data.

• Save Script: Export your workflow as a Python-compatible JSON script for reproducibility.

View Menu Tools#

The View menu also provides access to specialized analysis windows:

• View Session Log: Opens the Log Scripter (see above).

• View System Inspector: Opens the advanced interface for analyzing absorption lines. See the Absorption Systems tutorial for a full guide.

• View Identifications: Opens a summary table of all candidate lines found by the identify_lines recipe.

• View Script Console: Opens a Python console for running custom scripts on the current session data.

Saving and Closing#

When you have finished your analysis (or if you want to save your progress):

1. Save: Go to File > Save Session… or right-click the session in the list. This saves your work as an .acs2 file, preserving all your continuum fits and line lists.

2. Close: You can close a specific session via the right-click menu, or close the active session via File > Close Session.

Export to ASCII#

To save your current data in a human-readable format, go to File > Export to ASCII…. A dialog will appear allowing you to select exactly what to export:

• Spectrum (spec): Saves the Wavelength (\(x\)), Flux (\(y\)), Error (\(dy\)), Continuum (\(cont\)), and any other active spectral columns into a _spec.csv file.

• System List (systems): Saves your identified absorption lines (including Redshift, Column Density, Doppler Parameter, etc.) into a _systems.csv file.

You can choose to export entire structures or pick individual columns. The suggested filename will automatically adjust based on your selection, and Astrocook will warn you if you are about to overwrite existing files.

Import from ASCII#

If you have manipulated your exported _spec.csv data externally, you can bring it back into Astrocook by going to File > Import from ASCII….

• Astrocook will match the column headers in your CSV to the columns in the active session and overwrite them.

• Safety first: The imported file must have the exact same number of rows (pixels) as your current spectrum. Because this operates through the recipe pipeline, the import is fully undoable via the Log Scripter or Ctrl+Z (Cmd+Z).