teareduce 0.5.8__tar.gz → 0.6.0__tar.gz

{teareduce-0.5.8/src/teareduce.egg-info → teareduce-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.5.8
+Version: 0.6.0
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later
@@ -20,16 +20,17 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: astropy
-Requires-Dist: ccdproc
 Requires-Dist: lmfit
 Requires-Dist: matplotlib
-Requires-Dist: maskfill
-Requires-Dist: numpy>=1.22
+Requires-Dist: numpy>=2
 Requires-Dist: requests
 Requires-Dist: rich
 Requires-Dist: rich-argparse
 Requires-Dist: scipy
 Requires-Dist: tqdm
+Provides-Extra: cleanest
+Requires-Dist: ccdproc; extra == "cleanest"
+Requires-Dist: maskfill; extra == "cleanest"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Dynamic: license-file
@@ -67,6 +68,13 @@ $ . venv_teareduce/bin/activate
 (venv_teareduce) $ 
 ```
 
+If you are planning to use **tea-cleanest**, you need to install this package
+with extra dependencies. In this case employ:
+
+```shell
+(venv_teareduce) $ pip install 'teareduce[cleanest]'
+```
+
 ### Installing the package
 
 The latest stable version is available via de [PyPI repository](https://pypi.org/project/teareduce/):
@@ -94,6 +102,10 @@ 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__)
-0.4.3
+0.5.9
 ```
 
+Note that in PyPI there is a package called **tea** that provides utilities
+unrelated to **teareduce**. However, throughout the examples described
+in the documentation we are making use of ``import teareduce as tea``
+to define a convenient alias.

{teareduce-0.5.8 → teareduce-0.6.0}/README.md

@@ -31,6 +31,13 @@ $ . venv_teareduce/bin/activate
 (venv_teareduce) $ 
 ```
 
+If you are planning to use **tea-cleanest**, you need to install this package
+with extra dependencies. In this case employ:
+
+```shell
+(venv_teareduce) $ pip install 'teareduce[cleanest]'
+```
+
 ### Installing the package
 
 The latest stable version is available via de [PyPI repository](https://pypi.org/project/teareduce/):
@@ -58,6 +65,10 @@ 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__)
-0.4.3
+0.5.9
 ```
 
+Note that in PyPI there is a package called **tea** that provides utilities
+unrelated to **teareduce**. However, throughout the examples described
+in the documentation we are making use of ``import teareduce as tea``
+to define a convenient alias.

{teareduce-0.5.8 → teareduce-0.6.0}/pyproject.toml

@@ -2,7 +2,7 @@
 # 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 >= 61.0.0"]
+requires = ["setuptools >= 61.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -28,13 +28,12 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Astronomy",
 ]
 
+# Core dependencies (always installed)
 dependencies = [
     "astropy",
-    "ccdproc",
     "lmfit",
     "matplotlib",
-    "maskfill",
-    "numpy >= 1.22",
+    "numpy >= 2",
     "requests",
     "rich",
     "rich-argparse",
@@ -43,6 +42,12 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+# Version with dependencies needed to run the tea-cleanest script
+cleanest = [
+    "ccdproc",
+    "maskfill",
+]
+
 test = [
     "pytest",
 ]

teareduce-0.6.0/src/teareduce/cleanest/__init__.py

@@ -0,0 +1,19 @@
+#
+# 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 providing functions for cleaning astronomical images.
+Includes functions for interpolating over bad pixels,
+applying the L.A.Cosmic algorithm to detect cosmic ray pixels.
+"""
+
+from .interpolate import interpolate
+from .lacosmicpad import lacosmicpad
+from .mergemasks import merge_peak_tail_masks
+
+__all__ = ["interpolate", "lacosmicpad", "merge_peak_tail_masks"]

{teareduce-0.5.8 → teareduce-0.6.0}/src/teareduce/cleanest/__main__.py

@@ -10,7 +10,6 @@
 """Interactive Cosmic Ray cleaning tool."""
 
 import argparse
-from ast import arg
 import tkinter as tk
 from tkinter import filedialog
 from tkinter import simpledialog
@@ -93,10 +92,10 @@ def main():
             exit(1)
         print(f"Selected input FITS file: {args.input_fits}")
         args.extension = simpledialog.askstring(
-                "Select Extension",
-                f"\nEnter extension number or name for file:\n{Path(args.input_fits).name}",
-                initialvalue=args.extension,
-            )
+            "Select Extension",
+            f"\nEnter extension number or name for file:\n{Path(args.input_fits).name}",
+            initialvalue=args.extension,
+        )
         # Ask for auxiliary file if not provided
         if args.auxfile is None:
             use_auxfile = tk.messagebox.askyesno(
@@ -133,7 +132,13 @@ def main():
         exit(1)
 
     # Initialize Tkinter root
-    root = tk.Tk()
+    try:
+        root = tk.Tk()
+    except tk.TclError as e:
+        print("Error: Unable to initialize Tkinter. Make sure a display is available.")
+        print("Detailed error message:")
+        print(e)
+        exit(1)
     system = platform.system()
     if system == "Darwin":  # macOS
         # Center the window on the screen

teareduce-0.6.0/src/teareduce/cleanest/askextension.py

@@ -0,0 +1,85 @@
+#
+# Copyright 2025 Universidad Complutense de Madrid
+#
+# This file is part of teareduce
+#
+# SPDX-License-Identifier: GPL-3.0+
+# License-Filename: LICENSE.txt
+#
+
+"""Ask extension dialog for input FITS files."""
+
+from astropy.io import fits
+from tkinter import simpledialog, messagebox
+from pathlib import Path
+
+
+def ask_extension_input_image(filename, imgshape=None):
+    """Ask the user for the FITS extension to use for the input image.
+
+    Parameters
+    ----------
+    filename : str
+        The name of the FITS file.
+
+    Returns
+    -------
+    ext : int or str
+        The selected FITS extension (0-based index or name).
+    """
+    # Open the FITS file to get the list of extensions
+    try:
+        with fits.open(filename) as hdul:
+            ext_names = [hdu.name for hdu in hdul]
+            ext_indices = list(range(len(hdul)))
+            ext_bitpix = [hdu.header["BITPIX"] for hdu in hdul]
+    except Exception as e:
+        messagebox.showerror("Error", f"Unable to open FITS file '{filename}':\n{str(e)}")
+        return None
+
+    if len(ext_indices) == 1:
+        ext = 0
+    else:
+        # ask for the extension number in a dialog
+        ext_str = simpledialog.askstring(
+            "Select Extension",
+            f"\nEnter extension number (0-{len(ext_indices)-1}) for file:\n{Path(filename).name}\n"
+            f"Available extensions:\n"
+            + "\n".join(
+                [f"{i}: {name} (BITPIX={bitpix})" for i, name, bitpix in zip(ext_indices, ext_names, ext_bitpix)]
+            ),
+        )
+        if ext_str is None:
+            return None
+        # Validate the input
+        try:
+            ext = int(ext_str)
+            if ext < 0 or ext >= len(ext_indices):
+                raise ValueError("Extension number out of range")
+        except ValueError as e:
+            messagebox.showerror("Invalid Input", f"Error: {str(e)}")
+            return None
+
+    # check if ext is a valid array
+    with fits.open(filename) as hdul:
+        if hdul[ext] is None:
+            messagebox.showerror("Invalid Input", f"Extension {ext} does not exist in file '{filename}'")
+            return None
+        elif hdul[ext].data is None:
+            messagebox.showerror("Invalid Input", f"Extension {ext} in file '{filename}' has no data")
+            return None
+        elif hdul[ext].data.ndim != 2:
+            messagebox.showerror("Invalid Input", f"Extension {ext} in file '{filename}' is not 2D")
+            return None
+        elif hdul[ext].data.size == 0:
+            messagebox.showerror("Invalid Input", f"Extension {ext} in file '{filename}' has no data")
+            return None
+        elif imgshape is not None and (
+            hdul[ext].data.shape[0] != imgshape[0] or hdul[ext].data.shape[1] != imgshape[1]
+        ):
+            messagebox.showerror(
+                "Invalid Input",
+                f"Extension {ext} in file '{filename}' has unexpected shape {hdul[ext].data.shape}, expected {imgshape}",
+            )
+            return None
+    return ext