pyredshift 1.9__tar.gz

pyredshift-1.9/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Karl Glazebrook
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyredshift-1.9/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyredshift
+Version: 1.9
+Summary: Interactive redshifting of 1D astronomical spectra (Python successor of pdlredshift / redshift.f)
+Home-page: https://github.com/karlglazebrook/pyredshift
+Author: Karl Glazebrook
+License: MIT
+Keywords: astronomy spectroscopy redshift spectra interactive
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Environment :: MacOS X
+Classifier: Environment :: X11 Applications
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: astropy
+Requires-Dist: scipy
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# pyredshift
+
+Interactive redshifting of 1D astronomical spectra, by eye.
+
+`pyredshift` plots a spectrum histogram-style with a full-window crosshair
+cursor and overlays rest-frame line identifications that follow a trial
+redshift. Mark a feature you recognise, and the line labels jump to that
+redshift; refine, zoom, bin, smooth, fit a continuum and measure equivalent
+widths — all from single keypresses. It is the Python descendant of the
+author's venerable `redshift.f` (Fortran/Figaro, 1990s) via `pdlredshift`
+(Perl/PDL/PGPLOT), and deliberately keeps that fast keyboard-driven feel.
+
+![pyredshift showing an SDSS z=2.5 quasar in --retro mode](https://raw.githubusercontent.com/karlglazebrook/pyredshift/main/screenshot.png)
+
+*An SDSS quasar from [Example-Spectra](Example-Spectra/) at z = 2.48 and
+counting, in `--retro` mode: Lyα, CIV and CIII] lined up; the crosshair
+cursor mid-hunt.*
+
+## Install
+
+```
+pip install git+https://github.com/karlglazebrook/pyredshift
+```
+
+or from a checkout:
+
+```
+pip install .
+```
+
+This installs the `pyredshift` command into the active python's `bin/`
+(e.g. `anaconda3/bin`) and the `pyredshift` package into `site-packages`.
+Requires python ≥ 3.9 with numpy, matplotlib, astropy and scipy.
+
+## Usage
+
+```
+pyredshift spectrum.fits              # format auto-detected
+pyredshift spectrum.fits -f sdss      # force a format
+pyredshift spectrum.fits -z 2.19      # start from a known redshift
+pyredshift spectrum.fits --retro      # retro PGPLOT-style black background
+pyredshift spectrum.fits --microns    # keep micron wavelengths (no A conversion)
+```
+
+The file format is auto-detected by inspecting the FITS structure and
+column names/units:
+
+| Format     | Description                                                       |
+|------------|-------------------------------------------------------------------|
+| `fits`     | 1D (or 2D — row 1) FITS image with WCS; `CD1_1` overrides `CDELT1`, IRAF/SDSS log-λ flags handled |
+| `sdss`     | SDSS binary table (`LOGLAM`/`FLUX`, either case)                  |
+| `table`    | generic binary table with wave+flux columns; `TUNIT` (µm, nm, Å) converted automatically (aliases: `jwst`, `gabe`, `dja`) |
+| `xs`       | XSHOOTER 1D table spectrum (nm)                                   |
+| `xs2`      | XSHOOTER as a FITS image in extension 1                           |
+| `outthere` | OutThere multi-extension grism spectra, stitched and flat-calibrated |
+| `csv`      | comma-separated, header rows skipped                              |
+| `ascii`    | 2-column text                                                     |
+
+Wavelengths that look like microns are converted to Ångstroms; NaNs are
+treated as bad pixels and plot as gaps, with orange markers along the
+bottom of the frame.
+
+Real spectra to practice on are included in
+[Example-Spectra](Example-Spectra/) — the true redshifts are hidden in
+their FITS headers.
+
+### From a Jupyter notebook
+
+The interactive module also works straight from a notebook, given numpy
+arrays:
+
+```python
+from pyredshift import redshift as redshift_module
+z = redshift_module.redshift(wave, flux)
+```
+
+The interactive window opens *outside* the notebook (inline backends
+cannot deliver events to it) and the cell blocks until you quit with
+`q`; the final annotated view is then embedded in the cell output and
+the redshift returned. Any non-interactive backend (e.g. `%matplotlib
+inline`) is switched to a GUI backend for the session and restored
+afterwards — including if you interrupt the kernel mid-session.
+
+**Local kernels only**: the window opens on the machine where the
+kernel runs, so remote kernels (JupyterHub, cloud, ssh without X
+forwarding) cannot work — pyredshift detects this and says so rather
+than hanging or crashing the kernel.
+
+## Interaction
+
+Press `?` (or click the `?` button) for the full command reference — it
+opens as a themed page in your browser, with the complete line list and a
+short guide in separate tabs. The essentials:
+
+- **Identify a line**: put the crosshair on a feature and press `ESC`
+  followed by a shortcut key (`a` = Hα, `b` = Hβ, `l` = Lyα, `o` = [OII],
+  `c` = CIV ...) — or right-click the feature and pick the line from the
+  popup menu, or `g` to type any rest wavelength. Press `ESC ESC` on a
+  sharp line to refine the redshift; `=` enters a redshift directly.
+- **Navigate**: drag the mouse for a rubber-band zoom (a purely horizontal
+  drag zooms X only), `z`/`u` and `i`/`o` zoom about the cursor, `[` `]`
+  pan, `w` whole range, `a` autoscale, `h` home. The matplotlib toolbar
+  works too and stays in sync.
+- **Analyse**: `b` bin, `s` smooth, `_` iterative continuum fit,
+  `m` equivalent width and line flux, `B` zap artefacts, `p` print to PDF.
+- **Quit**: `q` — the final redshift is reported on the terminal.
+
+Line identifications come from `pyredshift.lines` (CSV: wavelength, name,
+label, matplotlib colour, comment — all vacuum wavelengths; a colour may
+be a `light/dark` pair for the two backgrounds), installed
+alongside the module and easy to customise. The window size and aspect
+ratio are remembered between runs in `~/.pyredshift.json`. A template
+spectrum can be overlaid with `t` (searched for in `$DATADIR`,
+`$NEWMODELS/Spectra`, then `~/Templates/Spectra`).
+
+## Layout
+
+```
+pyredshift            the command-line script: format detection and reading
+src/pyredshift/       the interactive module (redshift.py) + data files
+```
+
+The script prefers a `src/pyredshift/` found next to it or under the
+current directory, so a development checkout always runs its own code.
+
+## Credits
+
+Karl Glazebrook, Swinburne University of Technology.
+
+Lineage: `redshift.f` (FIGARO/Fortran, ~1992) → `pdlredshift` (Perl/PDL) →
+`pyredshift`. Ported with the assistance of Claude (Anthropic).
+
+MIT license — see [LICENSE](LICENSE).

pyredshift-1.9/README.md

@@ -0,0 +1,133 @@
+# pyredshift
+
+Interactive redshifting of 1D astronomical spectra, by eye.
+
+`pyredshift` plots a spectrum histogram-style with a full-window crosshair
+cursor and overlays rest-frame line identifications that follow a trial
+redshift. Mark a feature you recognise, and the line labels jump to that
+redshift; refine, zoom, bin, smooth, fit a continuum and measure equivalent
+widths — all from single keypresses. It is the Python descendant of the
+author's venerable `redshift.f` (Fortran/Figaro, 1990s) via `pdlredshift`
+(Perl/PDL/PGPLOT), and deliberately keeps that fast keyboard-driven feel.
+
+![pyredshift showing an SDSS z=2.5 quasar in --retro mode](https://raw.githubusercontent.com/karlglazebrook/pyredshift/main/screenshot.png)
+
+*An SDSS quasar from [Example-Spectra](Example-Spectra/) at z = 2.48 and
+counting, in `--retro` mode: Lyα, CIV and CIII] lined up; the crosshair
+cursor mid-hunt.*
+
+## Install
+
+```
+pip install git+https://github.com/karlglazebrook/pyredshift
+```
+
+or from a checkout:
+
+```
+pip install .
+```
+
+This installs the `pyredshift` command into the active python's `bin/`
+(e.g. `anaconda3/bin`) and the `pyredshift` package into `site-packages`.
+Requires python ≥ 3.9 with numpy, matplotlib, astropy and scipy.
+
+## Usage
+
+```
+pyredshift spectrum.fits              # format auto-detected
+pyredshift spectrum.fits -f sdss      # force a format
+pyredshift spectrum.fits -z 2.19      # start from a known redshift
+pyredshift spectrum.fits --retro      # retro PGPLOT-style black background
+pyredshift spectrum.fits --microns    # keep micron wavelengths (no A conversion)
+```
+
+The file format is auto-detected by inspecting the FITS structure and
+column names/units:
+
+| Format     | Description                                                       |
+|------------|-------------------------------------------------------------------|
+| `fits`     | 1D (or 2D — row 1) FITS image with WCS; `CD1_1` overrides `CDELT1`, IRAF/SDSS log-λ flags handled |
+| `sdss`     | SDSS binary table (`LOGLAM`/`FLUX`, either case)                  |
+| `table`    | generic binary table with wave+flux columns; `TUNIT` (µm, nm, Å) converted automatically (aliases: `jwst`, `gabe`, `dja`) |
+| `xs`       | XSHOOTER 1D table spectrum (nm)                                   |
+| `xs2`      | XSHOOTER as a FITS image in extension 1                           |
+| `outthere` | OutThere multi-extension grism spectra, stitched and flat-calibrated |
+| `csv`      | comma-separated, header rows skipped                              |
+| `ascii`    | 2-column text                                                     |
+
+Wavelengths that look like microns are converted to Ångstroms; NaNs are
+treated as bad pixels and plot as gaps, with orange markers along the
+bottom of the frame.
+
+Real spectra to practice on are included in
+[Example-Spectra](Example-Spectra/) — the true redshifts are hidden in
+their FITS headers.
+
+### From a Jupyter notebook
+
+The interactive module also works straight from a notebook, given numpy
+arrays:
+
+```python
+from pyredshift import redshift as redshift_module
+z = redshift_module.redshift(wave, flux)
+```
+
+The interactive window opens *outside* the notebook (inline backends
+cannot deliver events to it) and the cell blocks until you quit with
+`q`; the final annotated view is then embedded in the cell output and
+the redshift returned. Any non-interactive backend (e.g. `%matplotlib
+inline`) is switched to a GUI backend for the session and restored
+afterwards — including if you interrupt the kernel mid-session.
+
+**Local kernels only**: the window opens on the machine where the
+kernel runs, so remote kernels (JupyterHub, cloud, ssh without X
+forwarding) cannot work — pyredshift detects this and says so rather
+than hanging or crashing the kernel.
+
+## Interaction
+
+Press `?` (or click the `?` button) for the full command reference — it
+opens as a themed page in your browser, with the complete line list and a
+short guide in separate tabs. The essentials:
+
+- **Identify a line**: put the crosshair on a feature and press `ESC`
+  followed by a shortcut key (`a` = Hα, `b` = Hβ, `l` = Lyα, `o` = [OII],
+  `c` = CIV ...) — or right-click the feature and pick the line from the
+  popup menu, or `g` to type any rest wavelength. Press `ESC ESC` on a
+  sharp line to refine the redshift; `=` enters a redshift directly.
+- **Navigate**: drag the mouse for a rubber-band zoom (a purely horizontal
+  drag zooms X only), `z`/`u` and `i`/`o` zoom about the cursor, `[` `]`
+  pan, `w` whole range, `a` autoscale, `h` home. The matplotlib toolbar
+  works too and stays in sync.
+- **Analyse**: `b` bin, `s` smooth, `_` iterative continuum fit,
+  `m` equivalent width and line flux, `B` zap artefacts, `p` print to PDF.
+- **Quit**: `q` — the final redshift is reported on the terminal.
+
+Line identifications come from `pyredshift.lines` (CSV: wavelength, name,
+label, matplotlib colour, comment — all vacuum wavelengths; a colour may
+be a `light/dark` pair for the two backgrounds), installed
+alongside the module and easy to customise. The window size and aspect
+ratio are remembered between runs in `~/.pyredshift.json`. A template
+spectrum can be overlaid with `t` (searched for in `$DATADIR`,
+`$NEWMODELS/Spectra`, then `~/Templates/Spectra`).
+
+## Layout
+
+```
+pyredshift            the command-line script: format detection and reading
+src/pyredshift/       the interactive module (redshift.py) + data files
+```
+
+The script prefers a `src/pyredshift/` found next to it or under the
+current directory, so a development checkout always runs its own code.
+
+## Credits
+
+Karl Glazebrook, Swinburne University of Technology.
+
+Lineage: `redshift.f` (FIGARO/Fortran, ~1992) → `pdlredshift` (Perl/PDL) →
+`pyredshift`. Ported with the assistance of Claude (Anthropic).
+
+MIT license — see [LICENSE](LICENSE).

pyredshift-1.9/pyproject.toml

@@ -0,0 +1,6 @@
+# Minimal build-system declaration; the real metadata is in setup.py
+# (kept there because script-file installation with shebang rewriting
+# is a setup.py feature).
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

pyredshift-1.9/pyredshift

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+#!/usr/bin/env python3
+"""
+pyredshift - read a 1D spectrum in any of the usual formats and
+redshift it interactively.  Python port of the Perl 'pdlredshift'.
+
+Usage:
+    pyredshift spectrum.fits              # format auto-detected
+    pyredshift spectrum.fits -f sdss      # manual override
+    pyredshift spectrum.fits -z 2.19      # start at a known redshift
+
+Formats are auto-detected where possible by inspecting the FITS HDUs
+and column names/units, replacing the old mode zoo:
+    ascii     2 column ascii file
+    csv       comma separated, header rows skipped (NIRSPEC ERO data)
+    fits      1D (or 2D - row 1 used) FITS image with WCS; handles
+              CD1_1 overriding CDELT1 and IRAF/SDSS log-lambda flags
+    sdss      SDSS binary table (LOGLAM/FLUX, either case)
+    table     generic binary table with wave+flux columns; TUNIT
+              (um, nm, Angstrom...) converted automatically.
+              (aliases: jwst, jwst2, gabe, dja)
+    xs        XSHOOTER 1D table spectrum (WAVE in nm)
+    xs2       XSHOOTER as FITS image in extension 1 (Corentin's code)
+    outthere  OutThere multi-extension grism spectra: F115W/F150W/F200W
+              extensions stitched in wavelength order, flux/flat
+              calibrated, overlaps trimmed at the filter transitions
+"""
+
+import argparse
+import os
+import re
+import sys
+
+import numpy as np
+from astropy.io import fits
+from astropy import units as u
+
+# Dev override: a src/pyredshift package next to this script, or under the
+# current directory, is picked up in preference to the pip-installed one
+for _p in (os.path.join(os.path.dirname(os.path.abspath(__file__)), "src"),
+           os.path.join(os.getcwd(), "src")):
+    if os.path.isdir(os.path.join(_p, "pyredshift")):
+        sys.path.insert(0, _p)
+from pyredshift import redshift as redshift_module
+
+WAVE_COLS = ("wave", "wavelength", "lam", "lambda", "awav", "wav")
+FLUX_COLS = ("flux", "flam", "fnu", "spec", "counts")
+
+# Old pdlredshift mode names that the generic table reader now covers
+ALIASES = {"jwst": "table", "jwst2": "table", "gabe": "table", "dja": "table"}
+
+
+def wave_factor(unit_str):
+    """Conversion factor from a TUNIT string to Angstroms, or None."""
+    if not unit_str:
+        return None
+    try:
+        return float((1 * u.Unit(unit_str)).to(u.AA).value)
+    except Exception:
+        return None
+
+
+def read_ascii(fname):
+    print("Reading file %s as a 2 column ascii file" % fname)
+    wav, spec = np.loadtxt(fname, usecols=(0, 1), comments="#", unpack=True)
+    return wav, spec, True
+
+
+def read_csv(fname):
+    print("Reading file %s as a CSV table spectrum" % fname)
+    # Exclude headers: rows beginning with # or letters
+    wav, spec = [], []
+    with open(fname) as fh:
+        for line in fh:
+            if not line.strip() or re.match(r"^#|^\s*[A-Za-z]", line):
+                continue
+            parts = line.split(",")
+            try:
+                wav.append(float(parts[0]))
+                spec.append(float(parts[1]))
+            except (IndexError, ValueError):
+                continue
+    return np.array(wav), np.array(spec), True
+
+
+def first_table(hdul):
+    for hdu in hdul:
+        if getattr(hdu, "columns", None) is not None and hdu.data is not None:
+            return hdu
+    return None
+
+
+def first_image(hdul):
+    for hdu in hdul:
+        if hdu.is_image and hdu.data is not None and hdu.data.size > 1:
+            return hdu
+    return None
+
+
+def looks_outthere(hdul):
+    n = 0
+    for hdu in hdul:
+        if getattr(hdu, "columns", None) is None:
+            continue
+        extname = str(hdu.header.get("EXTNAME", ""))
+        if re.match(r"^F\d+W", extname) and "flat" in [c.lower() for c in hdu.columns.names]:
+            n += 1
+    return n >= 2
+
+
+def read_table(hdu, hint=""):
+    """Generic FITS table spectrum: find the wave/flux columns whatever
+    their case, use TUNIT to fix the wavelength units."""
+    low = {c.lower(): c for c in hdu.columns.names}
+
+    if "loglam" in low:  # The particular SDSS format FITS table
+        print("as a SDSS table spectrum")
+        wav = 10.0 ** np.asarray(hdu.data[low["loglam"]], float).ravel()
+        spec = np.asarray(hdu.data[low["flux"]], float).ravel()
+        return wav, spec
+
+    wcol = next((low[n] for n in WAVE_COLS if n in low), None)
+    fcol = next((low[n] for n in FLUX_COLS if n in low), None)
+    if wcol is None or fcol is None:
+        sys.exit("Cannot identify wavelength/flux columns among %s"
+                 % list(hdu.columns.names))
+    print("as a FITS table spectrum (columns %s, %s)" % (wcol, fcol), end="")
+    wav = np.asarray(hdu.data[wcol], float).ravel()
+    spec = np.asarray(hdu.data[fcol], float).ravel()
+
+    fac = wave_factor(hdu.columns[wcol].unit)
+    if fac is not None and fac != 1.0:
+        print("  [%s -> Angstroms]" % hdu.columns[wcol].unit, end="")
+        wav = wav * fac
+    elif fac is None and "SHOOT" in hint.upper():
+        print("  [XSHOOTER nm -> Angstroms]", end="")
+        wav = wav * 10.0
+    print()
+    return wav, spec
+
+
+def read_image(hdu):
+    print("as a FITS image spectrum", end="")
+    spec = np.asarray(hdu.data, float)
+    h = hdu.header
+    if spec.ndim == 2:  # Handle 2D case
+        print("   found 2D file, assuming row 1", end="")
+        spec = spec[0].copy()
+    x = np.arange(spec.size, dtype=float)
+    wav = x.copy()  # In case there is no WCS
+    has_wcs = "CRVAL1" in h
+    if has_wcs:
+        print(" found WCS", end="")
+        # See https://www.aanda.org/articles/aa/pdf/2002/45/aah3859.pdf
+        delt = h.get("CDELT1", 1.0)
+        if "CD1_1" in h:
+            delt = h["CD1_1"]  # CD1_1 overrides!
+        wav = (x - h.get("CRPIX1", 1.0) + 1) * delt + h["CRVAL1"]
+        # First is IRAF, second is SDSS convention
+        if h.get("DC-FLAG") or h.get("LOGSCALE") == 1:
+            print(" log scale", end="")
+            wav = 10.0 ** wav
+        else:
+            print(" linear scale", end="")
+    print()
+    return wav, spec, has_wcs
+
+
+def read_outthere(hdul):
+    """Read the F115W/F150W/F200W grism extensions and append them."""
+    print("as OutThere multi-extension grism spectra")
+    tabs = [hdu for hdu in hdul
+            if getattr(hdu, "columns", None) is not None
+            and str(hdu.header.get("EXTNAME", "")).startswith("F")]
+    tabs.sort(key=lambda hdu: hdu.header["EXTNAME"])  # EXTNAME order == wavelength order
+    wav = np.array([])
+    spec = np.array([])
+    for tab in tabs:
+        ext = tab.header["EXTNAME"]
+        wave = np.asarray(tab.data["wave"], float).ravel()
+        flux = np.asarray(tab.data["flux"], float).ravel()
+        flat = np.asarray(tab.data["flat"], float).ravel()
+        # Select wavelengths based on filter to avoid overlaps; these
+        # transitions are based on where one filter curve exceeds the other
+        keep = wave > 0  # Default select all
+        if ext == "F115W":
+            keep = wave <= 13040
+        if ext == "F150W":
+            keep = (wave > 13040) & (wave <= 17070)
+        if ext == "F200W":
+            keep = wave > 17070
+        with np.errstate(divide="ignore", invalid="ignore"):
+            wav = np.append(wav, wave[keep])
+            spec = np.append(spec, flux[keep] / flat[keep])
+    return wav, spec
+
+
+def read_spectrum(fname, fmt=None):
+    if not os.path.exists(fname):
+        sys.exit("File %s not found" % fname)
+    fmt = (fmt or "").lower()
+    fmt = ALIASES.get(fmt, fmt)
+
+    if fmt == "ascii":
+        return read_ascii(fname)
+    if fmt == "csv":
+        return read_csv(fname)
+
+    try:
+        hdul = fits.open(fname, memmap=False)
+    except Exception:
+        hdul = None
+
+    if hdul is None:  # Not FITS: csv or plain ascii
+        if fmt:
+            sys.exit("%s is not a FITS file, but format '%s' was requested"
+                     % (fname, fmt))
+        with open(fname) as fh:
+            for line in fh:
+                if line.strip() and not line.startswith("#"):
+                    if "," in line or fname.lower().endswith(".csv"):
+                        return read_csv(fname)
+                    return read_ascii(fname)
+        sys.exit("%s appears to be empty" % fname)
+
+    with hdul:
+        print("Reading file %s " % fname, end="")
+        instrume = str(hdul[0].header.get("INSTRUME", ""))
+        has_wcs = True  # tables always carry real wavelengths
+
+        if fmt in ("table", "sdss"):
+            wav, spec = read_table(first_table(hdul), instrume)
+        elif fmt == "xs":
+            print("as an XSHOOTER 1D table spectrum")
+            tab = hdul[1]
+            wav = np.asarray(tab.data["WAVE"], float).ravel() * 10
+            spec = np.asarray(tab.data["FLUX"], float).ravel()
+        elif fmt == "xs2":
+            wav, spec, has_wcs = read_image(hdul[1])
+            wav = wav * 10000.0
+        elif fmt == "outthere":
+            wav, spec = read_outthere(hdul)
+        elif fmt == "fits":
+            wav, spec, has_wcs = read_image(first_image(hdul))
+        elif fmt == "":  # Auto-detect from the HDU structure
+            if looks_outthere(hdul):
+                wav, spec = read_outthere(hdul)
+            else:
+                tab = first_table(hdul)
+                if tab is not None:
+                    wav, spec = read_table(tab, instrume)
+                else:
+                    img = first_image(hdul)
+                    if img is None:
+                        sys.exit("No spectrum found in FITS file")
+                    wav, spec, has_wcs = read_image(img)
+        else:
+            sys.exit("Unknown format '%s' (see pyredshift -h)" % fmt)
+
+    spec = np.asarray(spec, float)
+    spec[~np.isfinite(spec)] = np.nan  # NaNs plot as gaps downstream
+    return np.asarray(wav, float), spec, has_wcs
+
+
+def main():
+    ap = argparse.ArgumentParser(
+        prog="pyredshift",
+        description="Interactive redshifting of 1D spectra (port of pdlredshift).",
+        epilog="Formats: ascii csv fits sdss table (=jwst,jwst2,gabe,dja) "
+               "xs xs2 outthere.  Default is auto-detection.")
+    ap.add_argument("file", help="spectrum file (FITS, CSV or 2-column ascii)")
+    ap.add_argument("-f", "--format", default=None, metavar="FORMAT",
+                    help="force the input format instead of auto-detecting")
+    ap.add_argument("-z", "--redshift", type=float, default=None,
+                    help="initial redshift guess")
+    ap.add_argument("--retro", action="store_true",
+                    help="retro PGPLOT-style black background")
+    ap.add_argument("--microns", action="store_true",
+                    help="keep micron wavelengths (micron-mode display) "
+                         "instead of converting to Angstroms")
+    ap.add_argument("--dark", dest="retro", action="store_true",
+                    help=argparse.SUPPRESS)  # deprecated alias for --retro
+    args = ap.parse_args()
+
+    wav, spec, has_wcs = read_spectrum(args.file, args.format)
+
+    if np.nanmax(wav) < 100 and has_wcs and not args.microns:
+        print("  Detected microns -> Angstroms  (--microns to keep)")
+        wav = wav * 10000.0
+
+    z = redshift_module.redshift(wav, spec, args.redshift,
+                                 os.path.basename(args.file), dark=args.retro)
+    if z is not None:
+        print("Final redshift = %.6g" % z)
+
+
+if __name__ == "__main__":
+    main()

pyredshift-1.9/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

pyredshift-1.9/setup.py

@@ -0,0 +1,40 @@
+from setuptools import setup
+
+# pip install .   (from this directory)
+#
+# Installs:
+#   the pyredshift package (redshift.py + data files pyredshift.lines,
+#     pyredshift-help.html) -> site-packages/pyredshift/
+#   the pyredshift script -> the bin/ of whichever python runs the install
+#     (e.g. anaconda3/bin), with the shebang rewritten to that python.
+#
+# The package source lives in src/ (a file and a directory cannot share
+# the name 'pyredshift' at the top level).
+
+setup(
+    name="pyredshift",
+    version="1.9",
+    description="Interactive redshifting of 1D astronomical spectra "
+                "(Python successor of pdlredshift / redshift.f)",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
+    author="Karl Glazebrook",
+    url="https://github.com/karlglazebrook/pyredshift",
+    license="MIT",
+    classifiers=[
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Astronomy",
+        "License :: OSI Approved :: MIT License",
+        "Programming Language :: Python :: 3",
+        "Environment :: MacOS X",
+        "Environment :: X11 Applications",
+    ],
+    keywords="astronomy spectroscopy redshift spectra interactive",
+    packages=["pyredshift"],
+    package_dir={"": "src"},
+    package_data={"pyredshift": ["pyredshift.lines", "pyredshift-help.html"]},
+    scripts=["pyredshift"],
+    install_requires=["numpy", "matplotlib", "astropy", "scipy"],
+    python_requires=">=3.9",
+)

pyredshift-1.9/src/pyredshift/__init__.py

@@ -0,0 +1,5 @@
+"""pyredshift - interactive redshifting of 1D spectra.
+
+The interactive tool lives in pyredshift.redshift; the pyredshift script
+handles reading the many spectrum formats.
+"""