teareduce 0.4.2__py3-none-any.whl → 0.4.4__py3-none-any.whl

teareduce/__init__.py

@@ -14,6 +14,8 @@ from .ctext import ctext
 from .draw_rectangle import draw_rectangle
 from .elapsed_time import elapsed_time
 from .elapsed_time import elapsed_time_since
+from .histogram1d import hist_step
+from .histogram1d import plot_hist_step
 from .imshow import imshow
 from .imshow import imshowme
 from .numsplines import AdaptiveLSQUnivariateSpline
@@ -21,9 +23,9 @@ from .peaks_spectrum import find_peaks_spectrum, refine_peaks_spectrum
 from .polfit import polfit_residuals, polfit_residuals_with_sigma_rejection
 from .robust_std import robust_std
 from .sdistortion import fit_sdistortion
+from .simulateccdexposure import SimulateCCDExposure
 from .sliceregion import SliceRegion1D, SliceRegion2D, SliceRegion3D
 from .statsummary import ifc_statsummary, statsummary
-from .simulateccdexposure import SimulateCCDExposure
 from .version import VERSION
 from .wavecal import TeaWaveCalibration, apply_wavecal_ccddata
 from .write_array_to_fits import write_array_to_fits

teareduce/histogram1d.py

@@ -0,0 +1,85 @@
+#
+# Copyright 2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+# License-Filename: LICENSE.txt
+#
+
+"""Auxiliary function to display 1D histograms computed with numpy"""
+
+import numpy as np
+
+
+def plot_hist_step(ax, bins, h, color='C0', alpha=1.0, fill_color=None, fill_alpha=0.4):
+    """Plot histogram already computed.
+
+    Parameters
+    ----------
+    ax : matplotlib.axes.Axes
+        Axes to plot on.
+    bins : np.ndarray
+        Array of bin edges.
+    h : np.ndarray
+        Array of histogram values.
+    color : str, optional
+        Color of the histogram line, by default 'C0'.
+    alpha : float, optional
+        Transparency of the histogram line, by default 1.0.
+    fill_color : str, optional
+        Color to fill the histogram area, by default None (no fill).
+    fill_alpha : float, optional
+        Transparency of the filled area, by default 0.4.
+    """
+    # bin centers
+    xdum = (bins[:-1] + bins[1:]) / 2
+    ax.step(xdum, h, where='mid')
+    # draw vertical lines at the edges
+    ax.plot([bins[0], bins[0], xdum[0]], [0, h[0], h[0]], alpha=alpha, color=f'{color}', linestyle='-')
+    ax.plot([xdum[-1], bins[-1], bins[-1]], [h[-1], h[-1], 0], alpha=alpha, color=f'{color}', linestyle='-')
+    # fill area under the histogram
+    if fill_color is not None:
+        ax.fill_between(np.concatenate((np.array([bins[0]]), xdum, np.array([bins[-1]]))),
+                        np.concatenate((np.array([h[0]]), h, np.array([h[-1]]))),
+                        step='mid', alpha=fill_alpha, color=f'{fill_color}')
+
+
+def hist_step(ax, data, bins, color='C0', alpha=1.0, fill_color=None, fill_alpha=0.4):
+    """Compute and plot histogram of data.
+
+    Parameters
+    ----------
+    ax : matplotlib.axes.Axes
+        Axes to plot on.
+    data : np.ndarray
+        Data to compute the histogram from.
+    bins : int or np.ndarray
+        Number of bins or array of bin edges.
+    color : str, optional
+        Color of the histogram line, by default 'C0'.
+    alpha : float, optional
+        Transparency of the histogram line, by default 1.0.
+    fill_color : str, optional
+        Color to fill the histogram area, by default None (no fill).
+    fill_alpha : float, optional
+        Transparency of the filled area, by default 0.4.
+
+    Returns
+    -------
+    h : np.ndarray
+        Histogram values.
+    edges : np.ndarray
+        Bin edges of the histogram.
+    """
+
+    if isinstance(bins, int):
+        bins = np.linspace(np.min(data), np.max(data), bins + 1)
+    elif isinstance(bins, np.ndarray):
+        pass
+    else:
+        raise ValueError(f'Unexpected {bins=}')
+    h, edges = np.histogram(data, bins=bins)
+    plot_hist_step(ax, bins, h, color=color, alpha=alpha, fill_color=fill_color, fill_alpha=fill_alpha)
+
+    return h, edges

teareduce/imshow.py

@@ -101,6 +101,7 @@ def imshow(fig=None, ax=None, data=None,
     if ylabel is None:
         ylabel = 'Y axis (array index)'
 
+    wavecalib = False
     if crpix1 is not None and crval1 is not None and cdelt1 is not None and cunit1 is not None:
         if 'extent' in kwargs:
             raise ValueError('extent parameter can not be used with a wavelength calibration scale')
@@ -112,9 +113,12 @@ def imshow(fig=None, ax=None, data=None,
         u_pixel = Unit('pixel')
         xminwv = crval1 + (xmin * u_pixel - crpix1 + 1 * u_pixel) * cdelt1
         xmaxwv = crval1 + (xmax * u_pixel - crpix1 + 1 * u_pixel) * cdelt1
-        extent = [xminwv.to(cunitx).value, xmaxwv.to(cunitx).value, ymin, ymax]
+        xminwv = xminwv.to(cunitx).value
+        xmaxwv = xmaxwv.to(cunitx).value
+        extent = [xminwv, xmaxwv, ymin, ymax]
         xlabel = f'Wavelength ({cunitx})'
         aspect = 'auto'
+        wavecalib = True
     else:
         if 'extent' in kwargs:
             extent = kwargs['extent']
@@ -143,6 +147,19 @@ def imshow(fig=None, ax=None, data=None,
     if title is not None:
         ax.set_title(title)
 
+    # if a wavelength calibration is provided, display the index scale
+    # on the top horizontal axis
+    if wavecalib:
+
+        def index2coord(i):
+            return xminwv + (xmaxwv - xminwv) * i / (naxis1 - 1)
+
+        def coord2index(x):
+            return (naxis1 - 1) * (x - xminwv) / (xmaxwv - xminwv)
+
+        ax_top = ax.secondary_xaxis('top', functions=(coord2index, index2coord))
+        ax_top.set_xlabel('X axis (array index)')
+
     if colorbar:
         divider = make_axes_locatable(ax)
         cax = divider.append_axes("right", size="5%", pad=0.05, axes_class=Axes)

teareduce/tests/test_version.py

@@ -0,0 +1,8 @@
+
+from ..version import main, VERSION
+
+def test_main(capsys):
+    msg = f"Version: {VERSION}\n"
+    main()
+    captured = capsys.readouterr()
+    assert captured.out == msg

teareduce/version.py

@@ -9,7 +9,7 @@
 #
 """Module to define the version of the teareduce package."""
 
-VERSION = '0.4.2'
+VERSION = '0.4.4'
 
 
 def main():

{teareduce-0.4.2.dist-info → teareduce-0.4.4.dist-info}/METADATA

@@ -1,12 +1,11 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.2
+Version: 0.4.4
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later
 Project-URL: Homepage, https://github.com/nicocardiel/teareduce
 Project-URL: Repository, https://github.com/nicocardiel/teareduce.git
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -14,16 +13,16 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Development Status :: 3 - Alpha
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License (GPL)
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering :: Astronomy
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: astropy
 Requires-Dist: lmfit
 Requires-Dist: matplotlib
-Requires-Dist: numpy>=1.20
+Requires-Dist: numpy>=1.22
 Requires-Dist: scipy
 Requires-Dist: tqdm
 Provides-Extra: test
@@ -31,7 +30,24 @@ Requires-Dist: pytest; extra == "test"
 Dynamic: license-file
 
 # teareduce
-Utilities for astronomical data reduction
+
+Utilities for astronomical data reduction.
+
+This package is not intended to be a general-purpose image reduction code. It
+only includes specific operations required in certain steps of the traditional
+astronomical image reduction process that, at the time of its creation, were
+not available in more established packages such as
+[ccdproc](https://ccdproc.readthedocs.io/en/latest/). In addition, it also
+offers alternative ways to perform certain tasks that we have found to be more
+practical for use in Master’s level classes.
+
+
+## Documentation
+
+The documentation for this package is available at [this
+link](https://guaix.fis.ucm.es/~tea/teareduce-cookbook/_build/html/intro.html).
+It includes Juypter notebooks that can be easily downloaded and demonstrate the
+practical use of the defined functionality.
 
 ## Installing the code
 
@@ -73,5 +89,6 @@ The latest development version is available through [GitHub](https://github.com/
 (venv_teareduce) $ ipython
 In [1]: import teareduce as tea
 In [2]: print(tea.__version__)
-0.2.1
+0.4.3
 ```
+

{teareduce-0.4.2.dist-info → teareduce-0.4.4.dist-info}/RECORD

@@ -1,11 +1,12 @@
-teareduce/__init__.py,sha256=s3CE0R7rKhqBL_KJQD8Gzro_YzzWYZWZvTTKsJxCwBs,1229
+teareduce/__init__.py,sha256=u-6eZ9oz2reoSWxm1kf-9uj2VB4yERhh7fuE5gd4-RA,1304
 teareduce/avoid_astropy_warnings.py,sha256=2YgQ47pxsKYWDxUtzyEOfh3Is3aAHHmjJkuOa1JCDN4,648
 teareduce/correct_pincushion_distortion.py,sha256=Xpt03jtmJMyqik4ta95zMRE3Z6dVfzzHI2z5IDbtnMk,1685
 teareduce/cosmicrays.py,sha256=gLHgq9LdfNHmZ5n_FYxvxcGI2245TXGV-rFHSIogxPE,26877
 teareduce/ctext.py,sha256=8QP_KW7ueJ34IUyduVpy7nk-x0If5eilawf87icDMJA,2084
 teareduce/draw_rectangle.py,sha256=xlwcKIkl7e0U6sa9zWZr8t_WuWAte_UKIqCwZQ41x4Q,1922
 teareduce/elapsed_time.py,sha256=QWakPeiOUA__WpjjFREnodKqW1FZzVGWstab0N3Ro6k,1418
-teareduce/imshow.py,sha256=5j5RFoZOWBkF8CzUSLTR8-fNuuZHOFCMgH2CMOaDu50,4878
+teareduce/histogram1d.py,sha256=3hlvcI8XPRmZ27H_sFmyL26gIcbJozk07ELBKWtngQk,2835
+teareduce/imshow.py,sha256=P-TzdB8pOBnbFIMLu3MvKfBgSN91GsHTSh_02B0HsKI,5418
 teareduce/numsplines.py,sha256=1PpG-frdc9Qz3VRbC7XyZFWKmhus05ID4REtFnWDmUo,8049
 teareduce/peaks_spectrum.py,sha256=YPCJz8skJmIjWYqT7ZhBJGhnqPayFwy5xb7I9OHlUZI,9890
 teareduce/polfit.py,sha256=CGsrRsz_Du2aKxOcgXi36lpAZO04JyqCCUaxhC0C-Mk,14281
@@ -14,14 +15,15 @@ teareduce/sdistortion.py,sha256=5ZsZn4vD5Sw2aoqO8-NIOH7H89Zmh7ZDkow6YbAotHU,5916
 teareduce/simulateccdexposure.py,sha256=cdbpca6GVuM3d7R1LGzlIZZvjTq_jzrlkk_Cli7aouQ,24636
 teareduce/sliceregion.py,sha256=0h1xYcNG4mkJhR6bdaDe9pF2_MCuGeLJC7WVbbMZy8E,14977
 teareduce/statsummary.py,sha256=mtaM21d5aHvtLjCt_SSDMvD_fjI5nK21ZqxuDtcvldI,5426
-teareduce/version.py,sha256=wjxC_ZqjyEt9M9ZWw8WzCFiL0HIKJb6sqwgoZWMffL4,419
+teareduce/version.py,sha256=lKO2PdR2DtjUkH9hJBtVk-385YTx5NNIRltW67sZ0dk,419
 teareduce/wavecal.py,sha256=iiKG_RPW2CllwZxG5fTsyckE0Ec_IeZ6v7v2cQt6OeU,68706
 teareduce/write_array_to_fits.py,sha256=kWDrEH9coJ1yIu56oQJpWtDqJL4c8HGmssE9jle4e94,617
 teareduce/zscale.py,sha256=HuPYagTW55D7RtjPGc7HcibQlCx5oqLYHKoM6WEHG2g,1161
 teareduce/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 teareduce/tests/test_sliceregion.py,sha256=25dhS7yJ1z_3tgFLw21uOkNKuugyVA-8L1ehafSQjFg,1769
-teareduce-0.4.2.dist-info/licenses/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-teareduce-0.4.2.dist-info/METADATA,sha256=w4ubiClALKYDUznLttU83_EakmzY2xD2oEwK_js0h0U,2290
-teareduce-0.4.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-teareduce-0.4.2.dist-info/top_level.txt,sha256=7OkwtX9zNRkGJ7ACgjk4ESgC74qUYcS5O2qcO0v-Si4,10
-teareduce-0.4.2.dist-info/RECORD,,
+teareduce/tests/test_version.py,sha256=mKLnbXyvVNc1pATq5PxR8qeoFMPAFL_GilFV6IHLOi0,172
+teareduce-0.4.4.dist-info/licenses/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+teareduce-0.4.4.dist-info/METADATA,sha256=5njKTz4asc-xYbvhZwu8hZ2kFbjeLsfKnUVY6H8JTqo,3017
+teareduce-0.4.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+teareduce-0.4.4.dist-info/top_level.txt,sha256=7OkwtX9zNRkGJ7ACgjk4ESgC74qUYcS5O2qcO0v-Si4,10
+teareduce-0.4.4.dist-info/RECORD,,