teareduce 0.4.6__tar.gz → 0.4.8__tar.gz

{teareduce-0.4.6/src/teareduce.egg-info → teareduce-0.4.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.6
+Version: 0.4.8
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later

{teareduce-0.4.6 → teareduce-0.4.8}/pyproject.toml

@@ -47,7 +47,7 @@ Homepage = "https://github.com/nicocardiel/teareduce"
 Repository = "https://github.com/nicocardiel/teareduce.git"
 
 [project.scripts]
-tea-cleanest = "teareduce.cleanest:main"
+tea-cleanest = "teareduce.cleanest.__main__:main"
 
 [tool.setuptools.dynamic]
 version = {attr = "teareduce.version.VERSION"}

{teareduce-0.4.6 → teareduce-0.4.8}/src/teareduce/__init__.py

@@ -8,6 +8,7 @@
 #
 
 from .avoid_astropy_warnings import avoid_astropy_warnings
+from .cookbook.get_cookbook_file import get_cookbook_file
 from .correct_pincushion_distortion import correct_pincushion_distortion
 from .cosmicrays import cr2images, apply_cr2images_ccddata, crmedian
 from .ctext import ctext

teareduce-0.4.8/src/teareduce/cleanest/__main__.py

@@ -0,0 +1,49 @@
+#
+# Copyright 2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0+
+# License-Filename: LICENSE.txt
+#
+
+"""Interactive Cosmic Ray cleaning tool."""
+
+import argparse
+import tkinter as tk
+import os
+
+from .cosmicraycleanerapp import CosmicRayCleanerApp
+
+import matplotlib
+matplotlib.use("TkAgg")
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Interactive cosmic ray cleaner for FITS images.")
+    parser.add_argument("input_fits", help="Path to the FITS file to be cleaned.")
+    parser.add_argument("--extension", type=int, default=0,
+                        help="FITS extension to use (default: 0).")
+    parser.add_argument("--output_fits", type=str, default=None,
+                        help="Path to save the cleaned FITS file")
+    args = parser.parse_args()
+
+    if not os.path.isfile(args.input_fits):
+        print(f"Error: File '{args.input_fits}' does not exist.")
+        return
+    if args.output_fits is not None and os.path.isfile(args.output_fits):
+        print(f"Error: Output file '{args.output_fits}' already exists.")
+        return
+
+    # Initialize Tkinter root
+    root = tk.Tk()
+
+    # Create and run the application
+    CosmicRayCleanerApp(root, args.input_fits, args.extension, args.output_fits)
+
+    # Execute
+    root.mainloop()
+
+
+if __name__ == "__main__":
+    main()

teareduce-0.4.8/src/teareduce/cleanest/cosmicraycleanerapp.py

@@ -0,0 +1,203 @@
+#
+# Copyright 2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0+
+# License-Filename: LICENSE.txt
+#
+
+"""Define the CosmicRayCleanerApp class."""
+
+import tkinter as tk
+from tkinter import filedialog
+from tkinter import simpledialog
+
+from astropy.io import fits
+from ccdproc import cosmicray_lacosmic
+import matplotlib.pyplot as plt
+from matplotlib.backend_bases import key_press_handler
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
+import numpy as np
+import os
+
+from .reviewcosmicray import ReviewCosmicRay
+
+from ..imshow import imshow
+from ..zscale import zscale
+
+import matplotlib
+matplotlib.use("TkAgg")
+
+
+class CosmicRayCleanerApp():
+    """Main application class for cosmic ray cleaning."""
+
+    def __init__(self, root, input_fits, extension=0, output_fits=None):
+        """
+        Initialize the application.
+
+        Parameters
+        ----------
+        root : tk.Tk
+            The main Tkinter window.
+        input_fits : str
+            Path to the FITS file to be cleaned.
+        extension : int, optional
+            FITS extension to use (default is 0).
+        output_fits : str, optional
+            Path to save the cleaned FITS file (default is None, which prompts
+            for a save location).
+        """
+        self.root = root
+        self.root.title("Cosmic Ray Cleaner")
+        self.root.geometry("800x700+50+0")
+        self.input_fits = input_fits
+        self.extension = extension
+        self.output_fits = output_fits
+        self.load_fits_file()
+        self.create_widgets()
+
+    def load_fits_file(self):
+        try:
+            with fits.open(self.input_fits, mode='readonly') as hdul:
+                self.data = hdul[self.extension].data
+                if 'CRMASK' in hdul:
+                    self.mask_fixed = hdul['CRMASK'].data.astype(bool)
+                else:
+                    self.mask_fixed = np.zeros(self.data.shape, dtype=bool)
+        except Exception as e:
+            print(f"Error loading FITS file: {e}")
+
+    def save_fits_file(self):
+        if self.output_fits is None:
+            base, ext = os.path.splitext(self.input_fits)
+            suggested_name = f"{base}_cleaned"
+        else:
+            suggested_name, _ = os.path.splitext(self.output_fits)
+        self.output_fits = filedialog.asksaveasfilename(
+            initialdir=os.getcwd(),
+            title="Save cleaned FITS file",
+            defaultextension=".fits",
+            filetypes=[("FITS files", "*.fits"), ("All files", "*.*")],
+            initialfile=suggested_name
+        )
+        try:
+            with fits.open(self.input_fits, mode='readonly') as hdul:
+                hdul[self.extension].data = self.data
+                if 'CRMASK' in hdul:
+                    hdul['CRMASK'].data = self.mask_fixed.astype(np.uint8)
+                else:
+                    crmask_hdu = fits.ImageHDU(self.mask_fixed.astype(np.uint8), name='CRMASK')
+                    hdul.append(crmask_hdu)
+                hdul.writeto(self.output_fits, overwrite=True)
+            print(f"Cleaned data saved to {self.output_fits}")
+        except Exception as e:
+            print(f"Error saving FITS file: {e}")
+
+    def create_widgets(self):
+        # Row 1
+        self.button_frame1 = tk.Frame(self.root)
+        self.button_frame1.grid(row=0, column=0, pady=5)
+        self.run_lacosmic_button = tk.Button(self.button_frame1, text="Run L.A.Cosmic", command=self.run_lacosmic)
+        self.run_lacosmic_button.pack(side=tk.LEFT, padx=5)
+        self.save_button = tk.Button(self.button_frame1, text="Save cleaned FITS", command=self.save_fits_file)
+        self.save_button.pack(side=tk.LEFT, padx=5)
+
+        # Row 2
+        self.button_frame2 = tk.Frame(self.root)
+        self.button_frame2.grid(row=1, column=0, pady=5)
+        vmin, vmax = zscale(self.data)
+        self.vmin_button = tk.Button(self.button_frame2, text=f"vmin: {vmin:.2f}", command=self.set_vmin)
+        self.vmin_button.pack(side=tk.LEFT, padx=5)
+        self.vmax_button = tk.Button(self.button_frame2, text=f"vmax: {vmax:.2f}", command=self.set_vmax)
+        self.vmax_button.pack(side=tk.LEFT, padx=5)
+        self.stop_button = tk.Button(self.button_frame2, text="Stop program", command=self.stop_app)
+        self.stop_button.pack(side=tk.LEFT, padx=5)
+
+        # Main frame for figure and toolbar
+        self.main_frame = tk.Frame(self.root)
+        self.main_frame.grid(row=2, column=0, sticky="nsew")
+        self.root.grid_rowconfigure(2, weight=1)
+        self.root.grid_columnconfigure(0, weight=1)
+        self.main_frame.grid_rowconfigure(0, weight=1)
+        self.main_frame.grid_columnconfigure(0, weight=1)
+
+        # Create figure and axis
+        self.fig, self.ax = plt.subplots(figsize=(8, 6))
+        xlabel = 'X pixel (from 1 to NAXIS1)'
+        ylabel = 'Y pixel (from 1 to NAXIS2)'
+        extent = [0.5, self.data.shape[1] + 0.5, 0.5, self.data.shape[0] + 0.5]
+        self.image, _, _ = imshow(self.fig, self.ax, self.data, vmin=vmin, vmax=vmax,
+                                  xlabel=xlabel, ylabel=ylabel, extent=extent)
+        # Note: tight_layout should be called before defining the canvas
+        self.fig.tight_layout()
+
+        # Create canvas and toolbar
+        self.canvas = FigureCanvasTkAgg(self.fig, master=self.main_frame)
+        # The next two instructions prevent a segmentation fault when pressing "q"
+        self.canvas.mpl_disconnect(self.canvas.mpl_connect("key_press_event", key_press_handler))
+        self.canvas.mpl_connect("key_press_event", self.on_key)
+        self.canvas.mpl_connect("button_press_event", self.on_click)
+        canvas_widget = self.canvas.get_tk_widget()
+        canvas_widget.grid(row=0, column=0, sticky="nsew")
+
+        # Matplotlib toolbar
+        self.toolbar_frame = tk.Frame(self.main_frame)
+        self.toolbar_frame.grid(row=1, column=0, sticky="ew")
+        self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbar_frame)
+        self.toolbar.update()
+
+    def set_vmin(self):
+        old_vmin = self.get_vmin()
+        new_vmin = simpledialog.askfloat("Set vmin", "Enter new vmin:", initialvalue=old_vmin)
+        if new_vmin is None:
+            return
+        self.vmin_button.config(text=f"vmin: {new_vmin:.2f}")
+        self.image.set_clim(vmin=new_vmin)
+        self.canvas.draw()
+
+    def set_vmax(self):
+        old_vmax = self.get_vmax()
+        new_vmax = simpledialog.askfloat("Set vmax", "Enter new vmax:", initialvalue=old_vmax)
+        if new_vmax is None:
+            return
+        self.vmax_button.config(text=f"vmax: {new_vmax:.2f}")
+        self.image.set_clim(vmax=new_vmax)
+        self.canvas.draw()
+
+    def get_vmin(self):
+        return float(self.vmin_button.cget("text").split(":")[1])
+
+    def get_vmax(self):
+        return float(self.vmax_button.cget("text").split(":")[1])
+
+    def run_lacosmic(self):
+        self.run_lacosmic_button.config(state=tk.DISABLED)
+        self.stop_button.config(state=tk.DISABLED)
+        # Parameters for L.A.Cosmic can be adjusted as needed
+        _, mask_crfound = cosmicray_lacosmic(self.data, sigclip=4.5, sigfrac=0.3, objlim=5.0, verbose=True)
+        ReviewCosmicRay(
+            root=self.root,
+            data=self.data,
+            mask_fixed=self.mask_fixed,
+            mask_crfound=mask_crfound
+        )
+        print("L.A.Cosmic cleaning applied.")
+        self.run_lacosmic_button.config(state=tk.NORMAL)
+        self.stop_button.config(state=tk.NORMAL)
+
+    def stop_app(self):
+        self.root.quit()
+        self.root.destroy()
+
+    def on_key(self, event):
+        if event.key == 'q':
+            pass  # Ignore the "q" key to prevent closing the window
+        else:
+            print(f"Key pressed: {event.key}")
+
+    def on_click(self, event):
+        if event.inaxes:
+            x, y = event.xdata, event.ydata
+            print(f"Clicked at image coordinates: ({x:.2f}, {y:.2f})")

teareduce-0.4.6/src/teareduce/cleanest.py → teareduce-0.4.8/src/teareduce/cleanest/reviewcosmicray.py

@@ -7,25 +7,20 @@
 # License-Filename: LICENSE.txt
 #
 
-"""Interactive Cosmic Ray cleaning tool."""
+"""Define the ReviewCosmicRay class."""
 
-import argparse
 import tkinter as tk
-from tkinter import filedialog
 from tkinter import simpledialog
 
-from astropy.io import fits
-from ccdproc import cosmicray_lacosmic
 import matplotlib.pyplot as plt
 from matplotlib.backend_bases import key_press_handler
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
 import numpy as np
-import os
 from scipy import ndimage
 
-from .imshow import imshow
-from .sliceregion import SliceRegion2D
-from .zscale import zscale
+from ..imshow import imshow
+from ..sliceregion import SliceRegion2D
+from ..zscale import zscale
 
 import matplotlib
 matplotlib.use("TkAgg")
@@ -489,206 +484,3 @@ class ReviewCosmicRay():
                 self.remove_crosses_button.config(state=tk.NORMAL)
             # Update the display to reflect the change
             self.update_display()
-
-
-class CosmicRayCleanerApp():
-    """Main application class for cosmic ray cleaning."""
-
-    def __init__(self, root, input_fits, extension=0, output_fits=None):
-        """
-        Initialize the application.
-
-        Parameters
-        ----------
-        root : tk.Tk
-            The main Tkinter window.
-        input_fits : str
-            Path to the FITS file to be cleaned.
-        extension : int, optional
-            FITS extension to use (default is 0).
-        output_fits : str, optional
-            Path to save the cleaned FITS file (default is None, which prompts
-            for a save location).
-        """
-        self.root = root
-        self.root.title("Cosmic Ray Cleaner")
-        self.root.geometry("800x700+50+0")
-        self.input_fits = input_fits
-        self.extension = extension
-        self.output_fits = output_fits
-        self.load_fits_file()
-        self.create_widgets()
-
-    def load_fits_file(self):
-        try:
-            with fits.open(self.input_fits, mode='readonly') as hdul:
-                self.data = hdul[self.extension].data
-                if 'CRMASK' in hdul:
-                    self.mask_fixed = hdul['CRMASK'].data.astype(bool)
-                else:
-                    self.mask_fixed = np.zeros(self.data.shape, dtype=bool)
-        except Exception as e:
-            print(f"Error loading FITS file: {e}")
-
-    def save_fits_file(self):
-        if self.output_fits is None:
-            base, ext = os.path.splitext(self.input_fits)
-            suggested_name = f"{base}_cleaned"
-        else:
-            suggested_name, _ = os.path.splitext(self.output_fits)
-        self.output_fits = filedialog.asksaveasfilename(
-            initialdir=os.getcwd(),
-            title="Save cleaned FITS file",
-            defaultextension=".fits",
-            filetypes=[("FITS files", "*.fits"), ("All files", "*.*")],
-            initialfile=suggested_name
-        )
-        try:
-            with fits.open(self.input_fits, mode='readonly') as hdul:
-                hdul[self.extension].data = self.data
-                if 'CRMASK' in hdul:
-                    hdul['CRMASK'].data = self.mask_fixed.astype(np.uint8)
-                else:
-                    crmask_hdu = fits.ImageHDU(self.mask_fixed.astype(np.uint8), name='CRMASK')
-                    hdul.append(crmask_hdu)
-                hdul.writeto(self.output_fits, overwrite=True)
-            print(f"Cleaned data saved to {self.output_fits}")
-        except Exception as e:
-            print(f"Error saving FITS file: {e}")
-
-    def create_widgets(self):
-        # Row 1
-        self.button_frame1 = tk.Frame(self.root)
-        self.button_frame1.grid(row=0, column=0, pady=5)
-        self.run_lacosmic_button = tk.Button(self.button_frame1, text="Run L.A.Cosmic", command=self.run_lacosmic)
-        self.run_lacosmic_button.pack(side=tk.LEFT, padx=5)
-        self.save_button = tk.Button(self.button_frame1, text="Save cleaned FITS", command=self.save_fits_file)
-        self.save_button.pack(side=tk.LEFT, padx=5)
-
-        # Row 2
-        self.button_frame2 = tk.Frame(self.root)
-        self.button_frame2.grid(row=1, column=0, pady=5)
-        vmin, vmax = zscale(self.data)
-        self.vmin_button = tk.Button(self.button_frame2, text=f"vmin: {vmin:.2f}", command=self.set_vmin)
-        self.vmin_button.pack(side=tk.LEFT, padx=5)
-        self.vmax_button = tk.Button(self.button_frame2, text=f"vmax: {vmax:.2f}", command=self.set_vmax)
-        self.vmax_button.pack(side=tk.LEFT, padx=5)
-        self.stop_button = tk.Button(self.button_frame2, text="Stop program", command=self.stop_app)
-        self.stop_button.pack(side=tk.LEFT, padx=5)
-
-        # Main frame for figure and toolbar
-        self.main_frame = tk.Frame(self.root)
-        self.main_frame.grid(row=2, column=0, sticky="nsew")
-        self.root.grid_rowconfigure(2, weight=1)
-        self.root.grid_columnconfigure(0, weight=1)
-        self.main_frame.grid_rowconfigure(0, weight=1)
-        self.main_frame.grid_columnconfigure(0, weight=1)
-
-        # Create figure and axis
-        self.fig, self.ax = plt.subplots(figsize=(8, 6))
-        xlabel = 'X pixel (from 1 to NAXIS1)'
-        ylabel = 'Y pixel (from 1 to NAXIS2)'
-        extent = [0.5, self.data.shape[1] + 0.5, 0.5, self.data.shape[0] + 0.5]
-        self.image, _, _ = imshow(self.fig, self.ax, self.data, vmin=vmin, vmax=vmax,
-                                  xlabel=xlabel, ylabel=ylabel, extent=extent)
-        # Note: tight_layout should be called before defining the canvas
-        self.fig.tight_layout()
-
-        # Create canvas and toolbar
-        self.canvas = FigureCanvasTkAgg(self.fig, master=self.main_frame)
-        # The next two instructions prevent a segmentation fault when pressing "q"
-        self.canvas.mpl_disconnect(self.canvas.mpl_connect("key_press_event", key_press_handler))
-        self.canvas.mpl_connect("key_press_event", self.on_key)
-        self.canvas.mpl_connect("button_press_event", self.on_click)
-        canvas_widget = self.canvas.get_tk_widget()
-        canvas_widget.grid(row=0, column=0, sticky="nsew")
-
-        # Matplotlib toolbar
-        self.toolbar_frame = tk.Frame(self.main_frame)
-        self.toolbar_frame.grid(row=1, column=0, sticky="ew")
-        self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbar_frame)
-        self.toolbar.update()
-
-    def set_vmin(self):
-        old_vmin = self.get_vmin()
-        new_vmin = simpledialog.askfloat("Set vmin", "Enter new vmin:", initialvalue=old_vmin)
-        if new_vmin is None:
-            return
-        self.vmin_button.config(text=f"vmin: {new_vmin:.2f}")
-        self.image.set_clim(vmin=new_vmin)
-        self.canvas.draw()
-
-    def set_vmax(self):
-        old_vmax = self.get_vmax()
-        new_vmax = simpledialog.askfloat("Set vmax", "Enter new vmax:", initialvalue=old_vmax)
-        if new_vmax is None:
-            return
-        self.vmax_button.config(text=f"vmax: {new_vmax:.2f}")
-        self.image.set_clim(vmax=new_vmax)
-        self.canvas.draw()
-
-    def get_vmin(self):
-        return float(self.vmin_button.cget("text").split(":")[1])
-
-    def get_vmax(self):
-        return float(self.vmax_button.cget("text").split(":")[1])
-
-    def run_lacosmic(self):
-        self.run_lacosmic_button.config(state=tk.DISABLED)
-        self.stop_button.config(state=tk.DISABLED)
-        # Parameters for L.A.Cosmic can be adjusted as needed
-        _, mask_crfound = cosmicray_lacosmic(self.data, sigclip=4.5, sigfrac=0.3, objlim=5.0, verbose=True)
-        ReviewCosmicRay(
-            root=self.root,
-            data=self.data,
-            mask_fixed=self.mask_fixed,
-            mask_crfound=mask_crfound
-        )
-        print("L.A.Cosmic cleaning applied.")
-        self.run_lacosmic_button.config(state=tk.NORMAL)
-        self.stop_button.config(state=tk.NORMAL)
-
-    def stop_app(self):
-        self.root.quit()
-        self.root.destroy()
-
-    def on_key(self, event):
-        if event.key == 'q':
-            pass  # Ignore the "q" key to prevent closing the window
-        else:
-            print(f"Key pressed: {event.key}")
-
-    def on_click(self, event):
-        if event.inaxes:
-            x, y = event.xdata, event.ydata
-            print(f"Clicked at image coordinates: ({x:.2f}, {y:.2f})")
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Interactive cosmic ray cleaner for FITS images.")
-    parser.add_argument("input_fits", help="Path to the FITS file to be cleaned.")
-    parser.add_argument("--extension", type=int, default=0,
-                        help="FITS extension to use (default: 0).")
-    parser.add_argument("--output_fits", type=str, default=None,
-                        help="Path to save the cleaned FITS file")
-    args = parser.parse_args()
-
-    if not os.path.isfile(args.input_fits):
-        print(f"Error: File '{args.input_fits}' does not exist.")
-        return
-    if args.output_fits is not None and os.path.isfile(args.output_fits):
-        print(f"Error: Output file '{args.output_fits}' already exists.")
-        return
-
-    # Initialize Tkinter root
-    root = tk.Tk()
-
-    # Create and run the application
-    CosmicRayCleanerApp(root, args.input_fits, args.extension, args.output_fits)
-
-    # Execute
-    root.mainloop()
-
-
-if __name__ == "__main__":
-    main()

teareduce-0.4.8/src/teareduce/cookbook/get_cookbook_file.py

@@ -0,0 +1,34 @@
+#
+# Copyright 2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0+
+# License-Filename: LICENSE.txt
+
+import os
+import requests
+
+
+def get_cookbook_file(file_path, verbose=True):
+    """
+    Retrieve the contents of an auxiliary file.
+
+    The file is downloaded from the teareduce-cookbook GitHub repository
+
+    Parameters
+    ----------
+    file_path : str
+        The path to the auxiliary file.
+    verbose : bool, optional
+        If True, print a message when the file is downloaded.
+        Default is True.
+    """
+
+    url = f"https://raw.githubusercontent.com/nicocardiel/teareduce-cookbook/main/{file_path}"
+    response = requests.get(url)
+    local_filename = os.path.basename(file_path)
+    with open(local_filename, "wb") as f:
+        f.write(response.content)
+    if verbose:
+        print(f"File {local_filename} downloaded!")

{teareduce-0.4.6 → teareduce-0.4.8}/src/teareduce/sliceregion.py

@@ -43,7 +43,7 @@ class SliceRegion1D:
         Check if slice 'other' is within the parent slice.
     """
 
-    def __init__(self, region, mode=None):
+    def __init__(self, region, mode=None, naxis1=None):
         """Initialize SliceRegion1D.
 
         Parameters
@@ -54,6 +54,9 @@ class SliceRegion1D:
         mode : str
             Convention mode employed to define the slice.
             The two possible modes are 'fits' and 'python'.
+        naxis1 : int
+            The axis 1 size (length) of the data being sliced.
+            If provided, it is used to validate the slice region.
         """
         if isinstance(region, str):
             pattern = r'^\s*\[\s*\d+\s*:\s*\d+\s*\]\s*$'
@@ -82,17 +85,23 @@ class SliceRegion1D:
 
         if self.mode == 'fits':
             if region.stop < region.start:
-                raise ValueError(f'Invalid {region!r}')
+                raise ValueError(f'Invalid {region!r}: stop must be >= start')
             self.fits = region
             self.python = slice(region.start-1, region.stop)
         elif self.mode == 'python':
             if region.stop <= region.start:
-                raise ValueError(f'Invalid {region!r}')
+                raise ValueError(f'Invalid {region!r}: stop must be > start')
             self.fits = slice(region.start+1, region.stop)
             self.python = region
         else:
             raise ValueError(errmsg)
 
+        if naxis1 is not None:
+            if not (1 <= self.fits.start <= naxis1):
+                raise ValueError(f'Invalid start={self.fits.start} for naxis1={naxis1}')
+            if not (1 <= self.fits.stop <= naxis1+1):
+                raise ValueError(f'Invalid stop={self.fits.stop} for naxis1={naxis1}')
+
         s = self.fits
         self.fits_section = f'[{s.start}:{s.stop}]'
 
@@ -137,6 +146,10 @@ class SliceRegion1D:
         result = True
         return result
 
+    def length(self):
+        """Return the length of the slice."""
+        return self.python.stop - self.python.start
+
 
 class SliceRegion2D:
     """Store indices for slicing of 2D regions.
@@ -163,7 +176,7 @@ class SliceRegion2D:
     within(other)
         Check if slice 'other' is within the parent slice."""
 
-    def __init__(self, region, mode=None):
+    def __init__(self, region, mode=None, naxis1=None, naxis2=None):
         """Initialize SliceRegion2D.
 
         Parameters
@@ -175,6 +188,14 @@ class SliceRegion2D:
         mode : str
             Convention mode employed to define the slice.
             The two possible modes are 'fits' and 'python'.
+        naxis1 : int
+            The axis 1 size (length) of the data being sliced,
+            assuming the FITS convention.
+            If provided, it is used to validate the slice region.
+        naxis2 : int
+            The axis 2 size (length) of the data being sliced,
+            assuming the FITS convention.
+            If provided, it is used to validate the slice region.
         """
         if isinstance(region, str):
             pattern = r'^\s*\[\s*\d+\s*:\s*\d+\s*,\s*\d+\s*:\s*\d+\s*\]\s*$'
@@ -206,16 +227,16 @@ class SliceRegion2D:
 
         if self.mode == 'fits':
             if s1.stop < s1.start:
-                raise ValueError(f'Invalid {s1!r}')
+                raise ValueError(f'Invalid {s1!r}: stop must be >= start')
             if s2.stop < s2.start:
-                raise ValueError(f'Invalid {s2!r}')
+                raise ValueError(f'Invalid {s2!r}: stop must be >= start')
             self.fits = region
             self.python = 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}')
+                raise ValueError(f'Invalid {s1!r}: stop must be > start')
             if s2.stop <= s2.start:
-                raise ValueError(f'Invalid {s2!r}')
+                raise ValueError(f'Invalid {s2!r}: stop must be > start')
             self.fits = slice(s2.start+1, s2.stop), slice(s1.start+1, s1.stop)
             self.python = region
         else:
@@ -224,6 +245,17 @@ class SliceRegion2D:
         s1, s2 = self.fits
         self.fits_section = f'[{s1.start}:{s1.stop},{s2.start}:{s2.stop}]'
 
+        if naxis1 is not None:
+            if not (1 <= s1.start <= naxis1):
+                raise ValueError(f'Invalid start={s1.start} for naxis1={naxis1}')
+            if not (1 <= s1.stop <= naxis1):
+                raise ValueError(f'Invalid stop={s1.stop} for naxis1={naxis1}')
+        if naxis2 is not None:
+            if not (1 <= s2.start <= naxis2):
+                raise ValueError(f'Invalid start={s2.start} for naxis2={naxis2}')
+            if not (1 <= s2.stop <= naxis2):
+                raise ValueError(f'Invalid stop={s2.stop} for naxis2={naxis2}')
+
     def __eq__(self, other):
         return self.fits == other.fits and self.python == other.python
 
@@ -269,6 +301,11 @@ class SliceRegion2D:
         result = True
         return result
 
+    def area(self):
+        """Return the area of the slice."""
+        s1, s2 = self.python
+        return (s1.stop - s1.start) * (s2.stop - s2.start)
+
 
 class SliceRegion3D:
     """Store indices for slicing of 3D regions.
@@ -295,7 +332,7 @@ class SliceRegion3D:
     within(other)
         Check if slice 'other' is within the parent slice."""
 
-    def __init__(self, region, mode=None):
+    def __init__(self, region, mode=None, naxis1=None, naxis2=None, naxis3=None):
         """Initialize SliceRegion3D.
 
         Parameters
@@ -307,6 +344,18 @@ class SliceRegion3D:
         mode : str
             Convention mode employed to define the slice.
             The two possible modes are 'fits' and 'python'.
+        naxis1 : int
+            The axis 1 size (length) of the data being sliced,
+            assuming the FITS convention.
+            If provided, it is used to validate the slice region.
+        naxis2 : int
+            The axis 2 size (length) of the data being sliced,
+            assuming the FITS convention.
+            If provided, it is used to validate the slice region.
+        naxis3 : int
+            The axis 3 size (length) of the data being sliced,
+            assuming the FITS convention.
+            If provided, it is used to validate the slice region.
         """
         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*$'
@@ -338,20 +387,20 @@ class SliceRegion3D:
 
         if self.mode == 'fits':
             if s1.stop < s1.start:
-                raise ValueError(f'Invalid {s1!r}')
+                raise ValueError(f'Invalid {s1!r}: stop must be >= start')
             if s2.stop < s2.start:
-                raise ValueError(f'Invalid {s2!r}')
+                raise ValueError(f'Invalid {s2!r}: stop must be >= start')
             if s3.stop < s3.start:
-                raise ValueError(f'Invalid {s3!r}')
+                raise ValueError(f'Invalid {s3!r}: stop must be >= start')
             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}')
+                raise ValueError(f'Invalid {s1!r}: stop must be > start')
             if s2.stop <= s2.start:
-                raise ValueError(f'Invalid {s2!r}')
+                raise ValueError(f'Invalid {s2!r}: stop must be > start')
             if s3.stop <= s3.start:
-                raise ValueError(f'Invalid {s3!r}')
+                raise ValueError(f'Invalid {s3!r}: stop must be > start')
             self.fits = slice(s3.start+1, s3.stop), slice(s2.start+1, s2.stop), slice(s1.start+1, s1.stop)
             self.python = region
         else:
@@ -360,6 +409,22 @@ class SliceRegion3D:
         s1, s2, s3 = self.fits
         self.fits_section = f'[{s1.start}:{s1.stop},{s2.start}:{s2.stop},{s3.start}:{s3.stop}]'
 
+        if naxis1 is not None:
+            if not (1 <= s1.start <= naxis1):
+                raise ValueError(f'Invalid start={s1.start} for naxis1={naxis1}')
+            if not (1 <= s1.stop <= naxis1):
+                raise ValueError(f'Invalid stop={s1.stop} for naxis1={naxis1}')
+        if naxis2 is not None:
+            if not (1 <= s2.start <= naxis2):
+                raise ValueError(f'Invalid start={s2.start} for naxis2={naxis2}')
+            if not (1 <= s2.stop <= naxis2):
+                raise ValueError(f'Invalid stop={s2.stop} for naxis2={naxis2}')
+        if naxis3 is not None:
+            if not (1 <= s3.start <= naxis3):
+                raise ValueError(f'Invalid start={s3.start} for naxis3={naxis3}')
+            if not (1 <= s3.stop <= naxis3):
+                raise ValueError(f'Invalid stop={s3.stop} for naxis3={naxis3}')
+
     def __eq__(self, other):
         return self.fits == other.fits and self.python == other.python
 
@@ -408,3 +473,8 @@ class SliceRegion3D:
             return result
         result = True
         return result
+
+    def volume(self):
+        """Return the volume of the slice."""
+        s1, s2, s3 = self.python
+        return (s1.stop - s1.start) * (s2.stop - s2.start) * (s3.stop - s3.start)

teareduce-0.4.8/src/teareduce/tests/test_sliceregion.py

@@ -0,0 +1,116 @@
+# -*- 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]]]))
+
+
+def test_wrong_number_of_dimensions():
+    """Test the creation of a SliceRegion with wrong slices."""
+
+    try:
+        SliceRegion1D(np.s_[1:3, 2:4], mode='python')
+        assert False, "Expected ValueError for 1D slice with 2D input"
+    except ValueError:
+        pass
+
+    try:
+        SliceRegion2D(np.s_[1:3], mode='python')
+        assert False, "Expected ValueError for 2D slice with 1D input"
+    except ValueError:
+        pass
+
+    try:
+        SliceRegion3D(np.s_[1:3, 2:4], mode='python')
+        assert False, "Expected ValueError for 3D slice with 2D input"
+    except ValueError:
+        pass
+
+
+def test_wrong_limits_order():
+    """Test the creation of a SliceRegion with wrong limits."""
+
+    try:
+        SliceRegion1D(np.s_[10:5], mode='python')
+        assert False, "Expected ValueError for 1D slice with start > stop"
+    except ValueError:
+        pass
+
+    try:
+        SliceRegion2D(np.s_[1:3, 5:2], mode='python')
+        assert False, "Expected ValueError for 2D slice with start > stop in second dimension"
+    except ValueError:
+        pass
+
+    try:
+        SliceRegion3D(np.s_[1:3, 2:4, 6:1], mode='python')
+        assert False, "Expected ValueError for 3D slice with start > stop in third dimension"
+    except ValueError:
+        pass
+
+
+def test_limits_out_of_range():
+    """Test the creation of a SliceRegion with limits out of range."""
+
+    try:
+        SliceRegion1D(np.s_[-1:5], mode='python', naxis1=10)
+        assert False, "Expected ValueError for 1D slice with negative start"
+    except ValueError:
+        pass
+
+    try:
+        SliceRegion2D(np.s_[1:3, 2:25], mode='python', naxis1=10, naxis2=20)
+        assert False, "Expected ValueError for 2D slice with stop > naxis in second dimension"
+    except ValueError:
+        pass
+
+    try:
+        SliceRegion3D(np.s_[1:3, 2:4, 3:35], mode='python', naxis1=10, naxis2=20, naxis3=30)
+        assert False, "Expected ValueError for 3D slice with stop > naxis in third dimension"
+    except ValueError:
+        pass

{teareduce-0.4.6 → teareduce-0.4.8}/src/teareduce/version.py

@@ -9,7 +9,7 @@
 #
 """Module to define the version of the teareduce package."""
 
-VERSION = '0.4.6'
+VERSION = '0.4.8'
 
 
 def main():

{teareduce-0.4.6 → teareduce-0.4.8/src/teareduce.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.6
+Version: 0.4.8
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later

{teareduce-0.4.6 → teareduce-0.4.8}/src/teareduce.egg-info/SOURCES.txt

@@ -3,7 +3,6 @@ README.md
 pyproject.toml
 src/teareduce/__init__.py
 src/teareduce/avoid_astropy_warnings.py
-src/teareduce/cleanest.py
 src/teareduce/correct_pincushion_distortion.py
 src/teareduce/cosmicrays.py
 src/teareduce/ctext.py
@@ -29,6 +28,12 @@ src/teareduce.egg-info/dependency_links.txt
 src/teareduce.egg-info/entry_points.txt
 src/teareduce.egg-info/requires.txt
 src/teareduce.egg-info/top_level.txt
+src/teareduce/cleanest/__init__.py
+src/teareduce/cleanest/__main__.py
+src/teareduce/cleanest/cosmicraycleanerapp.py
+src/teareduce/cleanest/reviewcosmicray.py
+src/teareduce/cookbook/__init__.py
+src/teareduce/cookbook/get_cookbook_file.py
 src/teareduce/tests/__init__.py
 src/teareduce/tests/test_sliceregion.py
 src/teareduce/tests/test_version.py

teareduce-0.4.8/src/teareduce.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+tea-cleanest = teareduce.cleanest.__main__:main

teareduce-0.4.6/src/teareduce/tests/test_sliceregion.py

@@ -1,49 +0,0 @@
-# -*- 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-0.4.6/src/teareduce.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-tea-cleanest = teareduce.cleanest:main