teareduce 0.4.1__tar.gz → 0.4.3__tar.gz

{teareduce-0.4.1/src/teareduce.egg-info → teareduce-0.4.3}/PKG-INFO

@@ -1,34 +1,33 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.1
+Version: 0.4.3
 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 :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+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: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: astropy
-Requires-Dist: importlib_resources
 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
 Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
 
 # teareduce
 Utilities for astronomical data reduction

{teareduce-0.4.1 → teareduce-0.4.3}/pyproject.toml

@@ -2,8 +2,8 @@
 # Minimum requirements for the build system to execute.
 # (include packages imported in the different modules; otherwise
 # a ModuleNotFoundError is raised when using $ pip install -e .)
-requires = ["setuptools >= 43.0.0", "wheel", "numpy",
-            "astropy", "matplotlib", "scipy", "lmfit", "tqdm"]
+requires = ["setuptools >= 61.0.0", "wheel",
+            "astropy", "matplotlib", "numpy>=1.22","scipy", "lmfit", "tqdm"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -11,31 +11,29 @@ name = "teareduce"
 dynamic = ["version"]
 description = "Utilities for astronomical data reduction"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = {text = "GPL-3.0-or-later"}
 authors = [
   {name = "Nicolás Cardiel", email = "cardiel@ucm.es"},
 ]
 classifiers = [
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Development Status :: 3 - Alpha",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU General Public License (GPL)",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
     "Operating System :: OS Independent",
     "Topic :: Scientific/Engineering :: Astronomy",
 ]
 
 dependencies = [
     "astropy",
-    "importlib_resources",  # required with python < 3.9
     "lmfit",
     "matplotlib",
-    "numpy >= 1.20",
+    "numpy >= 1.22",
     "scipy",
     "tqdm",
 ]

{teareduce-0.4.1 → teareduce-0.4.3}/src/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
@@ -21,12 +23,12 @@ 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 .sliceregion import SliceRegion1D, SliceRegion2D
-from .statsummary import ifc_statsummary, statsummary
 from .simulateccdexposure import SimulateCCDExposure
-from .version import version
+from .sliceregion import SliceRegion1D, SliceRegion2D, SliceRegion3D
+from .statsummary import ifc_statsummary, statsummary
+from .version import VERSION
 from .wavecal import TeaWaveCalibration, apply_wavecal_ccddata
 from .write_array_to_fits import write_array_to_fits
 from .zscale import zscale
 
-__version__ = version
+__version__ = VERSION

{teareduce-0.4.1 → teareduce-0.4.3}/src/teareduce/cosmicrays.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2022-2024 Universidad Complutense de Madrid
+# Copyright 2022-2025 Universidad Complutense de Madrid
 #
 # This file is part of teareduce
 #
@@ -20,14 +20,17 @@ from .robust_std import robust_std
 from .sliceregion import SliceRegion2D
 
 
-def cr2images(data1, data2=None, ioffx=0, ioffy=0,
+def cr2images(data1, data2=None,
+              single_mode=False,
+              ioffx=0, ioffy=0,
               tsigma_peak=10, tsigma_tail=3, maxsize=None,
               list_skipped_regions=None,
               image_region=None,
               median_size=None,
               return_masks=False,
               debug_level=0,
-              zoom_region_imshow=None):
+              zoom_region_imshow=None,
+              aspect='equal'):
     """Remove cosmic rays from differences between 2 images.
 
     The input images must have the same shape. If only 1 image
@@ -42,6 +45,10 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
         Second image. If None, a median filtered version of 'data1'
         is employed. In this case, the parameter 'median_size' must
         be properly set.
+    single_mode : bool
+        If True, the function is used in single mode, i.e., only the
+        first image is cleaned (default=False). When the second image
+        is None, this parameter is automatically set to True.
     ioffx : int
         Integer offset (pixels) to place the second image on top of
         the first image in the horizontal direction (axis=1) in the
@@ -55,9 +62,13 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
     tsigma_tail : float
         Times sigma to detect additional pixels affected by cosmic
         rays.
-    maxsize : int
-        Maximum number of pixels affected by a single cosmic ray.
-        Above this number the detection is ignored.
+    maxsize : int or None
+        If not None, this parameter sets the maximum number of pixels
+        affected by cosmic rays in a single region. If the number of
+        pixels affected by a single cosmic ray is larger
+        than this value, the region is not cleaned. If None, all
+        regions are cleaned regardless of the number of pixels
+        affected by single cosmic rays.
     list_skipped_regions : list or None
         List of SliceRegion2D instances indicating image regions where
         detected cosmic rays will not be removed. The indices refer
@@ -80,6 +91,8 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
     zoom_region_imshow : SliceRegion2D instance or None
         If not None, display intermediate images, zooming in the
         indicated region.
+    aspect : str
+        Aspect ratio of the displayed images. Default is 'equal'.
 
     Returns
     -------
@@ -103,11 +116,9 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
         if (ioffx != 0) or (ioffy != 0):
             raise ValueError(f'ERROR: ioffx={ioffx} and ioffy={ioffy} must be zero!')
         if median_size is None:
-            raise ValueError(f'ERROR: you must specify median_size when only one image is available')
+            raise ValueError('ERROR: you must specify median_size when only one image is available')
         data2 = ndimage.median_filter(data1, size=median_size)
         single_mode = True
-    else:
-        single_mode = False
 
     if list_skipped_regions is not None and image_region is not None:
         raise ValueError('list_skipped_regions and useful_region are incompatible')
@@ -183,9 +194,6 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
     if shape1 != shape2:
         raise ValueError('ERROR: overlapping regions have different shape')
 
-    if maxsize is None:
-        maxsize = shape1[0] * shape1[1]
-
     # difference between the two overlapping regions
     diff = subdata1 - subdata2
     if debug_level > 0:
@@ -200,8 +208,20 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
         print(f'>>> Robust_std: {std:.3f}')
 
     # search for positive peaks (CR in data1)
+    if debug_level > 0:
+        print(f'>>> Searching for positive peaks (CR in data1) with tsigma_peak={tsigma_peak}')
     labels_pos_peak, no_cr_pos_peak = ndimage.label(diff > median + tsigma_peak * std)
+    if debug_level > 0:
+        print(f'>>> Found {no_cr_pos_peak} positive peaks')
+    # search for additional pixels affected by cosmic rays (tail)
+    if debug_level > 0:
+        print(f'>>> Searching for positive tails (CR in data1) with tsigma_tail={tsigma_tail}')
     labels_pos_tail, no_cr_pos_tail = ndimage.label(diff > median + tsigma_tail * std)
+    if debug_level > 0:
+        print(f'>>> Found {no_cr_pos_tail} positive tails')
+    # merge positive peaks and tails
+    if debug_level > 0:
+        print('>>> Merging positive peaks and tails')
     # set all CR peak pixels to 1
     mask_pos_peak = np.zeros_like(labels_pos_peak)
     mask_pos_peak[labels_pos_peak > 0] = 1
@@ -211,13 +231,21 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
     mask_pos_clean = np.zeros_like(labels_pos_peak)
     for icr in np.unique(labels_pos_tail_in_peak):
         if icr > 0:
-            npix_affected = np.sum(labels_pos_tail == icr)
-            if npix_affected <= maxsize:
+            if maxsize is None:
                 mask_pos_clean[labels_pos_tail == icr] = 1
+            else:
+                npix_affected = np.sum(labels_pos_tail == icr)
+                if npix_affected <= maxsize:
+                    mask_pos_clean[labels_pos_tail == icr] = 1
+
     # replace pixels affected by cosmic rays
+    if debug_level > 0:
+        print(f'>>> Replacing {np.sum(mask_pos_clean)} pixels affected by cosmic rays in data1')
     data1c = data1.copy()
     for item in np.argwhere(mask_pos_clean):
         data1c[item[0] + i1, item[1] + j1] = data2[item[0] + ii1, item[1] + jj1] + median
+    if debug_level > 0:
+        print('>>> Finished replacing pixels affected by cosmic rays in data1')
 
     if single_mode:
         data2c = data2.copy()
@@ -229,8 +257,20 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
         no_cr_neg_tail = 0
     else:
         # search for negative peaks (CR in data2)
+        if debug_level > 0:
+            print(f'>>> Searching for negative peaks (CR in data2) with tsigma_peak={tsigma_peak}')
         labels_neg_peak, no_cr_neg_peak = ndimage.label(diff < median - tsigma_peak * std)
+        if debug_level > 0:
+            print(f'>>> Found {no_cr_neg_peak} negative peaks')
+        # search for additional pixels affected by cosmic rays (tail)
+        if debug_level > 0:
+            print(f'>>> Searching for negative tails (CR in data2) with tsigma_tail={tsigma_tail}')
         labels_neg_tail, no_cr_neg_tail = ndimage.label(diff < median - tsigma_tail * std)
+        if debug_level > 0:
+            print(f'>>> Found {no_cr_neg_tail} negative tails')
+        # merge negative peaks and tails
+        if debug_level > 0:
+            print('>>> Merging negative peaks and tails')
         # set all CR peak pixels to 1
         mask_neg_peak = np.zeros_like(labels_neg_peak)
         mask_neg_peak[labels_neg_peak > 0] = 1
@@ -240,13 +280,20 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
         mask_neg_clean = np.zeros_like(labels_neg_peak)
         for icr in np.unique(labels_neg_tail_in_peak):
             if icr > 0:
-                npix_affected = np.sum(labels_neg_tail == icr)
-                if npix_affected <= maxsize:
+                if maxsize is None:
                     mask_neg_clean[labels_neg_tail == icr] = 1
+                else:
+                    npix_affected = np.sum(labels_neg_tail == icr)
+                    if npix_affected <= maxsize:
+                        mask_neg_clean[labels_neg_tail == icr] = 1
         # replace pixels affected by cosmic rays
+        if debug_level > 0:
+            print(f'>>> Replacing {np.sum(mask_neg_clean)} pixels affected by cosmic rays in data2')
         data2c = data2.copy()
         for item in np.argwhere(mask_neg_clean):
             data2c[item[0] + ii1, item[1] + jj1] = data1[item[0] + i1, item[1] + j1] - median
+        if debug_level > 0:
+            print('>>> Finished replacing pixels affected by cosmic rays in data2')
 
     # insert result in arrays with the original data shape
     mask_data1c = np.zeros((naxis2, naxis1), dtype=int)
@@ -269,7 +316,7 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
             hmin = max(min(diff.flatten()), median - 10*tsigma_peak*std)
             hmax = min(max(diff.flatten()), median + 10*tsigma_peak*std)
             bins = np.linspace(hmin, hmax, 100)
-            fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(12, 6))
+            fig, ax = plt.subplots(ncols=1, nrows=1)   # figsize=(12, 6)
             ax.hist(diff[zoom_region_imshow.python].flatten(), bins=bins)
             ax.set_xlabel('ADU')
             ax.set_ylabel('Number of pixels')
@@ -277,10 +324,10 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
             ax.set_yscale('log')
             plt.show()
             # display diff
-            fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(15, 15*naxis2/naxis1))
+            fig, ax = plt.subplots(ncols=1, nrows=1)  # figsize=(15, 15*naxis2/naxis1)
             vmin = median - tsigma_peak * std
             vmax = median + tsigma_peak * std
-            imshow(fig, ax, diff, vmin=vmin, vmax=vmax, cmap='seismic')
+            imshow(fig, ax, diff, vmin=vmin, vmax=vmax, cmap='seismic', aspect=aspect)
             ax.set_xlim([zoom_region_imshow.python[1].start, zoom_region_imshow.python[1].stop])
             ax.set_ylim([zoom_region_imshow.python[0].start, zoom_region_imshow.python[0].stop])
             ax.set_title('diff: overlapping data1 - data2')
@@ -291,7 +338,7 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
             data1, labels_pos_peak, labels_pos_tail, labels_pos_tail_in_peak, data1, data1c
         ]
         title_list1 = [
-            'data1', 'labels_pos_peak', 'labels_pos_tail', 'labels_pos_tail_in_peak', 
+            'data1', 'labels_pos_peak', 'labels_pos_tail', 'labels_pos_tail_in_peak',
             'data1 with C.R.', 'data1c'
         ]
         if debug_level == 1:
@@ -305,7 +352,7 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
                 data2, labels_neg_peak, labels_neg_tail, labels_neg_tail_in_peak, data2, data2c
             ]
             title_list2 = [
-                'data2', 'labels_neg_peak', 'labels_neg_tail', 'labels_neg_tail_in_peak', 
+                'data2', 'labels_neg_peak', 'labels_neg_tail', 'labels_neg_tail_in_peak',
                 'data2 with C.R.', 'data2c'
             ]
             if debug_level == 1:
@@ -329,7 +376,7 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
             for iplot, (image, title) in enumerate(zip(image_list, title_list)):
                 imgplot = image[zoom_region_imshow.python]
                 naxis2_, naxis1_ = imgplot.shape
-                fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(15, 15*naxis2_/naxis1_))
+                fig, ax = plt.subplots(ncols=1, nrows=1)  # figsize=(15, 15*naxis2_/naxis1_)
                 median_ = np.median(imgplot)
                 std_ = robust_std(imgplot)
                 if std_ == 0:
@@ -340,7 +387,7 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
                     vmin = median_ - 2 * std_
                     vmax = median_ + 5 * std_
                     cmap = 'gray'
-                imshow(fig, ax, image, vmin=vmin, vmax=vmax, cmap=cmap)
+                imshow(fig, ax, image, vmin=vmin, vmax=vmax, cmap=cmap, aspect=aspect)
                 ax.set_xlim([zoom_region_imshow.python[1].start, zoom_region_imshow.python[1].stop - 1])
                 ax.set_ylim([zoom_region_imshow.python[0].start, zoom_region_imshow.python[0].stop - 1])
                 ax.set_title(title)
@@ -385,7 +432,7 @@ def cr2images(data1, data2=None, ioffx=0, ioffy=0,
 def apply_cr2images_ccddata(infile1, infile2=None, outfile1=None, outfile2=None,
                             ioffx=0, ioffy=0, tsigma_peak=10, tsigma_tail=3,
                             list_skipped_regions=None, image_region=None,
-                            median_size=None, debug_level=0, zoom_region_imshow=None):
+                            median_size=None, debug_level=0, zoom_region_imshow=None, aspect='equal'):
     """Apply cr2images() to FITS files storing CCDData.
 
     The FITS file must contain:
@@ -444,6 +491,8 @@ def apply_cr2images_ccddata(infile1, infile2=None, outfile1=None, outfile2=None,
     zoom_region_imshow : SliceRegion2D instance or None
         If not None, display intermediate images, zooming in the
         indicated region.
+    aspect : str
+        Aspect ratio of the displayed images. Default is 'equal'.
 
     """
 
@@ -451,7 +500,7 @@ def apply_cr2images_ccddata(infile1, infile2=None, outfile1=None, outfile2=None,
         if (ioffx != 0) or (ioffy != 0):
             raise ValueError(f'ERROR: ioffx={ioffx} and ioffy={ioffy} must be zero!')
         if median_size is None:
-            raise ValueError(f'ERROR: you must specify median_size when only one image is available')
+            raise ValueError('ERROR: you must specify median_size when only one image is available')
 
     history_list = ['using cr2images:']
 
@@ -472,7 +521,8 @@ def apply_cr2images_ccddata(infile1, infile2=None, outfile1=None, outfile2=None,
             image_region=image_region,
             return_masks=True,
             debug_level=debug_level,
-            zoom_region_imshow=zoom_region_imshow
+            zoom_region_imshow=zoom_region_imshow,
+            aspect=aspect
         )
         ccdimage1_clean.mask[mask_data1c.astype(bool)] = True
         ccdimage2_clean.mask[mask_data2c.astype(bool)] = True
@@ -495,7 +545,8 @@ def apply_cr2images_ccddata(infile1, infile2=None, outfile1=None, outfile2=None,
             image_region=image_region,
             return_masks=True,
             debug_level=debug_level,
-            zoom_region_imshow=zoom_region_imshow
+            zoom_region_imshow=zoom_region_imshow,
+            aspect=aspect
         )
         ccdimage1_clean.mask[mask_data1c.astype(bool)] = True
         ccdimage2_uncertainty_array = ndimage.median_filter(ccdimage1.uncertainty.array, size=median_size)

{teareduce-0.4.1 → teareduce-0.4.3}/src/teareduce/elapsed_time.py

@@ -11,7 +11,7 @@
 from datetime import datetime
 import platform
 import sys
-from .version import version
+from .version import VERSION
 
 
 def elapsed_time(time_ini, time_end, osinfo=True):
@@ -36,7 +36,7 @@ def elapsed_time(time_ini, time_end, osinfo=True):
         print(f'node.............: {result.node}')
         print(f'Python executable: {sys.executable}')
 
-    print(f"teareduce version: {version}")
+    print(f"teareduce version: {VERSION}")
     print(f"Initial time.....: {time_ini}")
     print(f"Final time.......: {time_end}")
     print(f"Elapsed time.....: {time_end - time_ini}")
@@ -54,4 +54,4 @@ def elapsed_time_since(time_ini, osinfo=True):
     """
 
     time_end = datetime.now()
-    elapsed_time(time_ini, time_end)
+    elapsed_time(time_ini, time_end, osinfo=osinfo)

teareduce-0.4.3/src/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-0.4.1 → teareduce-0.4.3}/src/teareduce/simulateccdexposure.py

@@ -584,9 +584,9 @@ class SimulateCCDExposure:
 
         # BIAS and Readout Noise
         if np.isnan(self.bias.value).any():
-            raise ValueError(f"The parameter 'bias' contains NaN")
+            raise ValueError("The parameter 'bias' contains NaN")
         if np.isnan(self.readout_noise.value).any():
-            raise ValueError(f"The parameter 'readout_noise' contains NaN")
+            raise ValueError("The parameter 'readout_noise' contains NaN")
         image2d = self._rng.normal(
             loc=self.bias.value,
             scale=self.readout_noise.value
@@ -597,7 +597,7 @@ class SimulateCCDExposure:
 
         # DARK
         if np.isnan(self.dark.value).any():
-            raise ValueError(f"The parameter 'dark' contains NaN")
+            raise ValueError("The parameter 'dark' contains NaN")
         image2d += self.dark.value
         if imgtype == "dark":
             result.data = image2d
@@ -605,11 +605,11 @@ class SimulateCCDExposure:
 
         # OBJECT
         if np.isnan(self.flatfield).any():
-            raise ValueError(f"The parameter 'flatfield' contains NaN")
+            raise ValueError("The parameter 'flatfield' contains NaN")
         if np.isnan(self.data_model.value).any():
-            raise ValueError(f"The parameter 'data_model' contains NaN")
+            raise ValueError("The parameter 'data_model' contains NaN")
         if np.isnan(self.gain.value).any():
-            raise ValueError(f"The parameter 'gain' contains NaN")
+            raise ValueError("The parameter 'gain' contains NaN")
         if method.lower() == "poisson":
             # transform data_model from ADU to electrons,
             # generate Poisson distribution

{teareduce-0.4.1 → teareduce-0.4.3}/src/teareduce/sliceregion.py

@@ -6,10 +6,16 @@
 # SPDX-License-Identifier: GPL-3.0+
 # License-Filename: LICENSE.txt
 #
+"""Auxiliary classes to handle slicing regions in 1D, 2D, and 3D.
+
+These classes provide a way to define and manipulate slices in a 
+consistent manner, following both FITS and Python conventions.
+"""
 
-import numpy as np
 import re
 
+import numpy as np
+
 class SliceRegion1D:
     """Store indices for slicing of 1D regions.
     
@@ -35,7 +41,7 @@ class SliceRegion1D:
     within(other)
         Check if slice 'other' is within the parent slice.
     """
-    
+
     def __init__(self, region, mode=None):
         """Initialize SliceRegion1D.
 
@@ -58,21 +64,21 @@ class SliceRegion1D:
             region = np.s_[numbers_int[0]:numbers_int[1]]
 
         if isinstance(region, slice):
-            for number in [slice.start, slice.stop]:
+            for number in [region.start, region.stop]:
                 if number is None:
-                    raise ValueError(f'Invalid {slice!r}: you must specify start:stop in slice by number')
+                    raise ValueError(f'Invalid {region!r}: you must specify start:stop in slice by number')
         else:
-            raise ValueError(f'Object {region} of type {type(region)} is not a slice') 
-                             
+            raise ValueError(f'Object {region} of type {type(region)} is not a slice')
+
         if region.step not in [1, None]:
             raise ValueError(f'This class {self.__class__.__name__} '
                              'does not handle step != 1')
-                             
+
         errmsg = f'Invalid mode={mode}. Only "FITS" or "Python" (case insensitive) are valid'
         if mode is None:
             raise ValueError(errmsg)
         self.mode = mode.lower()
-                             
+
         if self.mode == 'fits':
             if region.stop < region.start:
                 raise ValueError(f'Invalid {region!r}')
@@ -129,7 +135,7 @@ class SliceRegion1D:
             return result
         result = True
         return result
-                     
+
 
 class SliceRegion2D:
     """Store indices for slicing of 2D regions.
@@ -140,9 +146,9 @@ class SliceRegion2D:
     Attributes
     ----------
     fits : slice
-        1D slice following the FITS convention.
+        2D slice following the FITS convention.
     python : slice
-        1D slice following the Python convention.
+        2D slice following the Python convention.
     mode : str
         Convention mode employed to define the slice.
         The two possible modes are 'fits' and 'python'.
@@ -157,7 +163,7 @@ class SliceRegion2D:
         Check if slice 'other' is within the parent slice."""
 
     def __init__(self, region, mode=None):
-        """Initialize SliceRegion1D.
+        """Initialize SliceRegion2D.
 
         Parameters
         ----------
@@ -182,13 +188,13 @@ class SliceRegion2D:
             s1, s2 = region
             for item in [s1, s2]:
                 if isinstance(item, slice):
-                    for number in [s1.start, s1.stop, s2.start, s2.stop]:
+                    for number in [item.start, item.stop]:
                         if number is None:
                             raise ValueError(f'Invalid {item!r}: you must specify start:stop in slice by number')
+                    if item.step not in [1, None]:
+                        raise ValueError(f'This class {self.__class__.__name__} does not handle step != 1')
                 else:
                     raise ValueError(f'Object {item} of type {type(item)} is not a slice')
-            if s1.step not in [1, None] or s2.step not in [1, None]:
-                raise ValueError(f'This class {self.__class__.__name__} does not handle step != 1')
         else:
             raise ValueError(f'This class {self.__class__.__name__} only handles 2D regions')
 
@@ -261,3 +267,143 @@ class SliceRegion2D:
             return result
         result = True
         return result
+
+
+class SliceRegion3D:
+    """Store indices for slicing of 3D regions.
+
+    The attributes .python and .fits provide the indices following
+    the Python and the FITS convention, respectively.
+
+    Attributes
+    ----------
+    fits : slice
+        3D slice following the FITS convention.
+    python : slice
+        3D slice following the Python convention.
+    mode : str
+        Convention mode employed to define the slice.
+        The two possible modes are 'fits' and 'python'.
+    fits_section : str
+        Resulting slice section in FITS convention:
+        '[num1:num2,num3:num4,num5:num6]'. This string is defined after
+        successfully initializing the SliceRegion3D instance.
+
+    Methods
+    -------
+    within(other)
+        Check if slice 'other' is within the parent slice."""
+
+    def __init__(self, region, mode=None):
+        """Initialize SliceRegion3D.
+
+        Parameters
+        ----------
+        region : slice or str
+            Slice region. It can be provided as np.s_[num1:num2, num3:num4, num5:num6],
+            as a tuple (slice(num1, num2), slice(num3, num4), slice(num5, num6)),
+            or as a string '[num1:num2, num3:num4, num5:num6]'
+        mode : str
+            Convention mode employed to define the slice.
+            The two possible modes are 'fits' and 'python'.
+        """
+        if isinstance(region, str):
+            pattern = r'^\s*\[\s*\d+\s*:\s*\d+\s*,\s*\d+\s*:\s*\d+\s*,\s*\d+\s*:\s*\d+\s*\]\s*$'
+            if not re.match(pattern, region):
+                raise ValueError(f"Invalid {region!r}. It must match '[num:num, num:num, num:num]'")
+            # extract numbers and generate np.s_[num:num, num:num, num:num]
+            numbers_str = re.findall(r'\d+', region)
+            numbers_int = list(map(int, numbers_str))
+            region = np.s_[numbers_int[0]:numbers_int[1], numbers_int[2]:numbers_int[3], numbers_int[4]:numbers_int[5]]
+
+        if isinstance(region, tuple) and len(region) == 3:
+            s1, s2, s3 = region
+            for item in [s1, s2, s3]:
+                if isinstance(item, slice):
+                    for number in [item.start, item.stop]:
+                        if number is None:
+                            raise ValueError(f'Invalid {item!r}: you must specify start:stop in slice by number')
+                    if item.step not in [1, None]:
+                        raise ValueError(f'This class {self.__class__.__name__} does not handle step != 1')
+                else:
+                    raise ValueError(f'Object {item} of type {type(item)} is not a slice')
+        else:
+            raise ValueError(f'This class {self.__class__.__name__} only handles 3D regions')
+
+        errmsg = f'Invalid mode={mode}. Only "FITS" or "Python" (case insensitive) are valid'
+        if mode is None:
+            raise ValueError(errmsg)
+        self.mode = mode.lower()
+
+        if self.mode == 'fits':
+            if s1.stop < s1.start:
+                raise ValueError(f'Invalid {s1!r}')
+            if s2.stop < s2.start:
+                raise ValueError(f'Invalid {s2!r}')
+            if s3.stop < s3.start:
+                raise ValueError(f'Invalid {s3!r}')
+            self.fits = region
+            self.python = slice(s3.start-1, s3.stop), slice(s2.start-1, s2.stop), slice(s1.start-1, s1.stop)
+        elif self.mode == 'python':
+            if s1.stop <= s1.start:
+                raise ValueError(f'Invalid {s1!r}')
+            if s2.stop <= s2.start:
+                raise ValueError(f'Invalid {s2!r}')
+            if s3.stop <= s3.start:
+                raise ValueError(f'Invalid {s3!r}')
+            self.fits = slice(s3.start+1, s3.stop), slice(s2.start+1, s2.stop), slice(s1.start+1, s1.stop)
+            self.python = region
+        else:
+            raise ValueError(errmsg)
+
+        s1, s2, s3 = self.fits
+        self.fits_section = f'[{s1.start}:{s1.stop},{s2.start}:{s2.stop},{s3.start}:{s3.stop}]'
+
+    def __eq__(self, other):
+        return self.fits == other.fits and self.python == other.python
+
+    def __repr__(self):
+        if self.mode == 'fits':
+            return (f'{self.__class__.__name__}('
+                    f'{self.fits!r}, mode="fits")')
+        else:
+            return (f'{self.__class__.__name__}('
+                    f'{self.python!r}, mode="python")')
+
+    def within(self, other):
+        """Determine if slice 'other' is within the parent slice.
+
+        Parameters
+        ----------
+        other : SliceRegion3D
+            New instance for which we want to determine
+            if it is within the parent SliceRegion3D instance.
+
+        Returns
+        -------
+        result : bool
+            Return True if 'other' is within the parent slice.
+            False otherwise.
+        """
+        if isinstance(other, self.__class__):
+            pass
+        else:
+            raise ValueError(f'Object {other} of type {type(other)} is not a {self.__class__.__name__}')
+
+        s1, s2, s3 = self.python
+        s1_other, s2_other, s3_other = other.python
+        result = False
+        if s1.start < s1_other.start:
+            return result
+        if s1.stop > s1_other.stop:
+            return result
+        if s2.start < s2_other.start:
+            return result
+        if s2.stop > s2_other.stop:
+            return result
+        if s3.start < s3_other.start:
+            return result
+        if s3.stop > s3_other.stop:
+            return result
+        result = True
+        return result

teareduce-0.4.3/src/teareduce/tests/test_sliceregion.py

@@ -0,0 +1,49 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright 2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+# License-Filename: LICENSE.txt
+#
+"""Tests for the SliceRegion class."""
+
+import numpy as np
+
+from ..sliceregion import SliceRegion1D, SliceRegion2D, SliceRegion3D
+
+
+def test_slice_region_creation():
+    """Test the creation of a SliceRegion."""
+
+    region1d = SliceRegion1D(np.s_[1:10], mode='python')
+    assert region1d.fits == slice(2, 10, None)
+    assert region1d.python == slice(1, 10, None)
+    assert region1d.fits_section == '[2:10]'
+
+    region2d = SliceRegion2D(np.s_[1:10, 2:20], mode='python')
+    assert region2d.fits == (slice(3, 20, None), slice(2, 10, None))
+    assert region2d.python == (slice(1, 10, None), slice(2, 20, None))
+    assert region2d.fits_section == '[3:20,2:10]'
+
+    region3d = SliceRegion3D(np.s_[1:10, 2:20, 3:30], mode='python')
+    assert region3d.fits == (slice(4, 30, None), slice(3, 20, None), slice(2, 10, None))
+    assert region3d.python == (slice(1, 10, None), slice(2, 20, None), slice(3, 30, None))
+    assert region3d.fits_section == '[4:30,3:20,2:10]'
+
+def test_slice_values():
+    """Test the values of the slices in different modes."""
+
+    array1d = np.arange(10)
+
+    region1d = SliceRegion1D(np.s_[1:3], mode='python')
+    assert np.all(array1d[region1d.python] == np.array([1, 2]))
+
+    array2d = np.arange(12).reshape(3, 4)
+    region2d = SliceRegion2D(np.s_[1:3, 2:3], mode='python')
+    assert np.all(array2d[region2d.python] == np.array([[6], [10]]))
+
+    array3d = np.arange(24).reshape(3, 4, 2)
+    region3d = SliceRegion3D(np.s_[1:3, 2:4, 1:2], mode='python')
+    assert np.all(array3d[region3d.python] == np.array([[[13], [15]], [[21], [23]]]))

teareduce-0.4.3/src/teareduce/version.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright 2023-2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+# License-Filename: LICENSE.txt
+#
+"""Module to define the version of the teareduce package."""
+
+VERSION = '0.4.3'
+
+
+def main():
+    """Prints the version of the teareduce package."""
+    print('Version: ' + VERSION)
+
+
+if __name__ == "__main__":
+    main()

{teareduce-0.4.1 → teareduce-0.4.3/src/teareduce.egg-info}/PKG-INFO

@@ -1,34 +1,33 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.1
+Version: 0.4.3
 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 :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+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: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: astropy
-Requires-Dist: importlib_resources
 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
 Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
 
 # teareduce
 Utilities for astronomical data reduction

{teareduce-0.4.1 → teareduce-0.4.3}/src/teareduce.egg-info/SOURCES.txt

@@ -1,7 +1,6 @@
 LICENSE.txt
 README.md
 pyproject.toml
-src/teareduce/SimulateCCDExposure.py
 src/teareduce/__init__.py
 src/teareduce/avoid_astropy_warnings.py
 src/teareduce/correct_pincushion_distortion.py
@@ -9,6 +8,7 @@ src/teareduce/cosmicrays.py
 src/teareduce/ctext.py
 src/teareduce/draw_rectangle.py
 src/teareduce/elapsed_time.py
+src/teareduce/histogram1d.py
 src/teareduce/imshow.py
 src/teareduce/numsplines.py
 src/teareduce/peaks_spectrum.py
@@ -26,4 +26,6 @@ src/teareduce.egg-info/PKG-INFO
 src/teareduce.egg-info/SOURCES.txt
 src/teareduce.egg-info/dependency_links.txt
 src/teareduce.egg-info/requires.txt
-src/teareduce.egg-info/top_level.txt
+src/teareduce.egg-info/top_level.txt
+src/teareduce/tests/__init__.py
+src/teareduce/tests/test_sliceregion.py

{teareduce-0.4.1 → teareduce-0.4.3}/src/teareduce.egg-info/requires.txt

@@ -1,8 +1,7 @@
 astropy
-importlib_resources
 lmfit
 matplotlib
-numpy>=1.20
+numpy>=1.22
 scipy
 tqdm
 

teareduce-0.4.1/src/teareduce/version.py

@@ -1,19 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright 2023-2024 Universidad Complutense de Madrid
-#
-# This file is part of teareduce
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-# License-Filename: LICENSE.txt
-#
-
-version = '0.4.1'
-
-
-def main():
-    print('Version: ' + version)
-
-
-if __name__ == "__main__":
-    main()