teareduce 0.5.7__tar.gz → 0.5.9__tar.gz

{teareduce-0.5.7/src/teareduce.egg-info → teareduce-0.5.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.5.7
+Version: 0.5.9
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later
@@ -20,15 +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: 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
@@ -66,6 +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/):
@@ -93,6 +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-0.5.7 → teareduce-0.5.9}/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-0.5.7 → teareduce-0.5.9}/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]
@@ -28,12 +28,12 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Astronomy",
 ]
 
+# Core dependencies (always installed)
 dependencies = [
     "astropy",
-    "ccdproc",
     "lmfit",
     "matplotlib",
-    "numpy >= 1.22",
+    "numpy >= 2",
     "requests",
     "rich",
     "rich-argparse",
@@ -42,6 +42,12 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+# Version with dependencies needed to run the tea-cleanest script
+cleanest = [
+    "ccdproc",
+    "maskfill",
+]
+
 test = [
     "pytest",
 ]

teareduce-0.5.9/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-0.5.7 → teareduce-0.5.9}/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

{teareduce-0.5.7 → teareduce-0.5.9}/src/teareduce/cleanest/cosmicraycleanerapp.py

@@ -17,6 +17,14 @@ from tkinter import simpledialog
 import sys
 
 from astropy.io import fits
+try:
+    from maskfill import maskfill
+except ModuleNotFoundError as e:
+    raise ModuleNotFoundError(
+        "The 'teareduce.cleanest' module requires the 'ccdproc' and 'maskfill' packages. "
+        "Please install teareduce with the 'cleanest' extra dependencies: "
+        "`pip install teareduce[cleanest]`."
+    ) from e
 import matplotlib.pyplot as plt
 from matplotlib.backend_bases import key_press_handler
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
@@ -773,6 +781,21 @@ class CosmicRayCleanerApp(ImageDisplay):
                     # upate mask_crfound by eliminating the cleaned pixels
                     self.mask_crfound[mask_crfound_region] = False
                     data_has_been_modified = True
+                elif cleaning_method == "maskfill":
+                    # Replace detected CR pixels with local median values
+                    smoothed_output, _ = maskfill(
+                        input_image=self.data,
+                        mask=mask_crfound_region,
+                        size=3,
+                        operator="median",
+                        smooth=True,
+                    )
+                    self.data[mask_crfound_region] = smoothed_output[mask_crfound_region]
+                    # update mask_fixed to include the newly fixed pixels
+                    self.mask_fixed[mask_crfound_region] = True
+                    # upate mask_crfound by eliminating the cleaned pixels
+                    self.mask_crfound[mask_crfound_region] = False
+                    data_has_been_modified = True
                 elif cleaning_method == "auxdata":
                     if self.auxdata is None:
                         print("No auxiliary data available. Cleaning skipped!")

{teareduce-0.5.7 → teareduce-0.5.9}/src/teareduce/cleanest/definitions.py

@@ -43,7 +43,7 @@ lacosmic_default_dict = {
 }
 
 # Default parameters for cleaning methods
-VALID_CLEANING_METHODS = ["x interp.", "y interp.", "surface interp.", "median", "mean", "lacosmic", "auxdata"]
+VALID_CLEANING_METHODS = ["x interp.", "y interp.", "surface interp.", "median", "mean", "lacosmic", "maskfill", "auxdata"]
 
 # Maximum pixel distance to consider when finding closest CR pixel
 MAX_PIXEL_DISTANCE_TO_CR = 15

{teareduce-0.5.7 → teareduce-0.5.9}/src/teareduce/cleanest/interpolationeditor.py

@@ -97,6 +97,7 @@ class InterpolationEditor:
             "median": "a-median",
             "mean": "a-mean",
             "lacosmic": "lacosmic",
+            "maskfill": "maskfill",
             "auxdata": "auxdata",
         }
         self.check_interp_methods()

{teareduce-0.5.7 → teareduce-0.5.9}/src/teareduce/cleanest/lacosmicpad.py

@@ -9,7 +9,14 @@
 
 """Execute LACosmic algorithm on a padded image."""
 
-from ccdproc import cosmicray_lacosmic
+try:
+    from ccdproc import cosmicray_lacosmic
+except ModuleNotFoundError as e:
+    raise ModuleNotFoundError(
+        "The 'teareduce.cleanest' module requires the 'ccdproc' and 'maskfill' packages. "
+        "Please install teareduce with the 'cleanest' extra dependencies: "
+        "`pip install teareduce[cleanest]`."
+    ) from e
 import numpy as np
 
 

{teareduce-0.5.7 → teareduce-0.5.9}/src/teareduce/cleanest/reviewcosmicray.py

@@ -13,6 +13,14 @@ import tkinter as tk
 from tkinter import messagebox
 from tkinter import simpledialog
 
+try:
+    from maskfill import maskfill
+except ModuleNotFoundError as e:
+    raise ModuleNotFoundError(
+        "The 'teareduce.cleanest' module requires the 'ccdproc' and 'maskfill' packages. "
+        "Please install teareduce with the 'cleanest' extra dependencies: "
+        "`pip install teareduce[cleanest]`."
+    ) from e
 import matplotlib.pyplot as plt
 from matplotlib.backend_bases import key_press_handler
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
@@ -150,7 +158,7 @@ class ReviewCosmicRay(ImageDisplay):
             self.root.minsize(1000, 700)
         else:
             # self.root.geometry("800x700+100+100")  # This does not work in Fedora
-            self.root.minsize(800, 700)
+            self.root.minsize(900, 700)
         self.root.update_idletasks()
         self.root.geometry("+100+100")
         self.data = data
@@ -224,6 +232,8 @@ class ReviewCosmicRay(ImageDisplay):
             self.interp_l_button.config(state=tk.DISABLED)
         if self.cleandata_lacosmic is None:
             self.interp_l_button.config(state=tk.DISABLED)
+        self.interp_maskfill_button = tk.Button(self.button_frame2, text="mas[k]fill", command=self.use_maskfill)
+        self.interp_maskfill_button.pack(side=tk.LEFT, padx=5)
         self.interp_aux_button = tk.Button(self.button_frame2, text="[a]ux. data", command=self.use_auxdata)
         self.interp_aux_button.pack(side=tk.LEFT, padx=5)
         if self.auxdata is None:
@@ -246,7 +256,7 @@ class ReviewCosmicRay(ImageDisplay):
         if self.auxdata is not None:
             self.fig, (self.ax_aux, self.ax) = plt.subplots(ncols=2, figsize=(11, 5.5), constrained_layout=True)
         else:
-            self.fig, self.ax = plt.subplots(figsize=(8, 5.5), constrained_layout=True)
+            self.fig, self.ax = plt.subplots(figsize=(9, 5.5), constrained_layout=True)
         self.canvas = FigureCanvasTkAgg(self.fig, master=self.root)
         self.canvas.get_tk_widget().pack(padx=5, pady=5)
         # The next two instructions prevent a segmentation fault when pressing "q"
@@ -368,15 +378,9 @@ class ReviewCosmicRay(ImageDisplay):
 
     def set_buttons_after_cleaning_cr(self):
         """Set the state of buttons after cleaning a cosmic ray."""
+        self.disable_interpolation_buttons()
         self.restore_cr_button.config(state=tk.NORMAL)
         self.remove_crosses_button.config(state=tk.DISABLED)
-        self.interp_x_button.config(state=tk.DISABLED)
-        self.interp_y_button.config(state=tk.DISABLED)
-        self.interp_s_button.config(state=tk.DISABLED)
-        self.interp_d_button.config(state=tk.DISABLED)
-        self.interp_m_button.config(state=tk.DISABLED)
-        self.interp_l_button.config(state=tk.DISABLED)
-        self.interp_aux_button.config(state=tk.DISABLED)
 
     def interp_x(self):
         """Perform x-direction interpolation to clean a cosmic ray."""
@@ -461,6 +465,27 @@ class ReviewCosmicRay(ImageDisplay):
         self.set_buttons_after_cleaning_cr()
         self.update_display(cleaned=True)
 
+    def use_maskfill(self):
+        """Use maskfill cleaned data to clean a cosmic ray."""
+        print(f"Maskfill interpolation of cosmic ray {self.cr_index}")
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        mask = np.zeros(self.data.shape, dtype=bool)
+        for iy, ix in zip(ycr_list, xcr_list):
+            mask[iy, ix] = True
+        smoothed_output, _ = maskfill(
+            input_image=self.data,
+            mask=mask,
+            size=3,
+            operator="median",
+            smooth=True,
+        )
+        for iy, ix in zip(ycr_list, xcr_list):
+            self.data[iy, ix] = smoothed_output[iy, ix]
+            self.mask_fixed[iy, ix] = True
+        self.num_cr_cleaned += 1
+        self.set_buttons_after_cleaning_cr()
+        self.update_display(cleaned=True)
+
     def use_auxdata(self):
         """Use auxiliary data to clean a cosmic ray."""
         if self.auxdata is None:
@@ -481,34 +506,21 @@ class ReviewCosmicRay(ImageDisplay):
         for iy, ix in zip(ycr_list, xcr_list):
             self.cr_labels[iy, ix] = 0
         print(f"Removed all pixels of cosmic ray {self.cr_index}")
-        self.remove_crosses_button.config(state=tk.DISABLED)
-        self.interp_x_button.config(state=tk.DISABLED)
-        self.interp_y_button.config(state=tk.DISABLED)
-        self.interp_s_button.config(state=tk.DISABLED)
-        self.interp_d_button.config(state=tk.DISABLED)
-        self.interp_m_button.config(state=tk.DISABLED)
-        self.interp_l_button.config(state=tk.DISABLED)
-        self.interp_aux_button.config(state=tk.DISABLED)
+        self.disable_interpolation_buttons()
         self.update_display()
 
     def restore_cr(self):
         """Restore all pixels of the current cosmic ray to their original values."""
         ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        if len(xcr_list) == 0:
+            print(f"No pixels to restore for cosmic ray {self.cr_index}")
+            return
         for iy, ix in zip(ycr_list, xcr_list):
             self.data[iy, ix] = self.data_original[iy, ix]
             self.mask_fixed[iy, ix] = False
-            self.interp_x_button.config(state=tk.NORMAL)
-            self.interp_y_button.config(state=tk.NORMAL)
-            self.interp_s_button.config(state=tk.NORMAL)
-            self.interp_d_button.config(state=tk.NORMAL)
-            self.interp_m_button.config(state=tk.NORMAL)
-            if self.cleandata_lacosmic is not None:
-                if self.last_dilation is None or self.last_dilation == 0:
-                    self.interp_l_button.config(state=tk.NORMAL)
-            if self.auxdata is not None:
-                self.interp_aux_button.config(state=tk.NORMAL)
         print(f"Restored all pixels of cosmic ray {self.cr_index}")
         self.num_cr_cleaned -= 1
+        self.enable_interpolation_buttons()
         self.remove_crosses_button.config(state=tk.NORMAL)
         self.restore_cr_button.config(state=tk.DISABLED)
         self.update_display()
@@ -524,16 +536,7 @@ class ReviewCosmicRay(ImageDisplay):
             return  # important: do not remove (to avoid errors)
         self.first_plot = True
         self.restore_cr_button.config(state=tk.DISABLED)
-        self.interp_x_button.config(state=tk.NORMAL)
-        self.interp_y_button.config(state=tk.NORMAL)
-        self.interp_s_button.config(state=tk.NORMAL)
-        self.interp_d_button.config(state=tk.NORMAL)
-        self.interp_m_button.config(state=tk.NORMAL)
-        if self.cleandata_lacosmic is not None:
-            if self.last_dilation is None or self.last_dilation == 0:
-                self.interp_l_button.config(state=tk.NORMAL)
-        if self.auxdata is not None:
-            self.interp_aux_button.config(state=tk.NORMAL)
+        self.enable_interpolation_buttons()
         self.remove_crosses_button.config(state=tk.NORMAL)
         self.update_display()
 
@@ -566,6 +569,9 @@ class ReviewCosmicRay(ImageDisplay):
         elif event.key == "l":
             if self.interp_l_button.cget("state") != "disabled":
                 self.use_lacosmic()
+        elif event.key == "k":
+            if self.interp_maskfill_button.cget("state") != "disabled":
+                self.use_maskfill()
         elif event.key == "a":
             if self.interp_aux_button.cget("state") != "disabled":
                 self.use_auxdata()
@@ -595,25 +601,35 @@ class ReviewCosmicRay(ImageDisplay):
                 print(f"Pixel ({ix+1}, {iy+1}), with signal {self.data[iy, ix]}, marked as cosmic ray.")
             xcr_list, ycr_list = np.where(self.cr_labels == self.cr_index)
             if len(xcr_list) == 0:
-                self.interp_x_button.config(state=tk.DISABLED)
-                self.interp_y_button.config(state=tk.DISABLED)
-                self.interp_s_button.config(state=tk.DISABLED)
-                self.interp_d_button.config(state=tk.DISABLED)
-                self.interp_m_button.config(state=tk.DISABLED)
-                self.interp_l_button.config(state=tk.DISABLED)
-                self.interp_aux_button.config(state=tk.DISABLED)
+                self.disable_interpolation_buttons()
                 self.remove_crosses_button.config(state=tk.DISABLED)
             else:
-                self.interp_x_button.config(state=tk.NORMAL)
-                self.interp_y_button.config(state=tk.NORMAL)
-                self.interp_s_button.config(state=tk.NORMAL)
-                self.interp_d_button.config(state=tk.NORMAL)
-                self.interp_m_button.config(state=tk.NORMAL)
-                if self.cleandata_lacosmic is not None:
-                    if self.last_dilation is None or self.last_dilation == 0:
-                        self.interp_l_button.config(state=tk.NORMAL)
-                if self.auxdata is not None:
-                    self.interp_aux_button.config(state=tk.NORMAL)
+                self.enable_interpolation_buttons()
                 self.remove_crosses_button.config(state=tk.NORMAL)
             # Update the display to reflect the change
             self.update_display()
+
+    def disable_interpolation_buttons(self):
+        """Disable all interpolation buttons."""
+        self.interp_x_button.config(state=tk.DISABLED)
+        self.interp_y_button.config(state=tk.DISABLED)
+        self.interp_s_button.config(state=tk.DISABLED)
+        self.interp_d_button.config(state=tk.DISABLED)
+        self.interp_m_button.config(state=tk.DISABLED)
+        self.interp_l_button.config(state=tk.DISABLED)
+        self.interp_maskfill_button.config(state=tk.DISABLED)
+        self.interp_aux_button.config(state=tk.DISABLED)
+
+    def enable_interpolation_buttons(self):
+        """Enable all interpolation buttons."""
+        self.interp_x_button.config(state=tk.NORMAL)
+        self.interp_y_button.config(state=tk.NORMAL)
+        self.interp_s_button.config(state=tk.NORMAL)
+        self.interp_d_button.config(state=tk.NORMAL)
+        self.interp_m_button.config(state=tk.NORMAL)
+        if self.cleandata_lacosmic is not None:
+             if self.last_dilation is None or self.last_dilation == 0:
+                 self.interp_l_button.config(state=tk.NORMAL)
+        self.interp_maskfill_button.config(state=tk.NORMAL)
+        if self.auxdata is not None:
+            self.interp_aux_button.config(state=tk.NORMAL)

{teareduce-0.5.7 → teareduce-0.5.9}/src/teareduce/version.py

@@ -9,7 +9,7 @@
 #
 """Module to define the version of the teareduce package."""
 
-VERSION = '0.5.7'
+VERSION = '0.5.9'
 
 
 def main():

{teareduce-0.5.7 → teareduce-0.5.9/src/teareduce.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.5.7
+Version: 0.5.9
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later
@@ -20,15 +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: 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
@@ -66,6 +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/):
@@ -93,6 +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-0.5.7 → teareduce-0.5.9}/src/teareduce.egg-info/requires.txt

@@ -1,13 +1,16 @@
 astropy
-ccdproc
 lmfit
 matplotlib
-numpy>=1.22
+numpy>=2
 requests
 rich
 rich-argparse
 scipy
 tqdm
 
+[cleanest]
+ccdproc
+maskfill
+
 [test]
 pytest

teareduce-0.5.7/src/teareduce/cleanest/__init__.py

@@ -1,12 +0,0 @@
-#
-# 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
-#
-
-from .interpolate import interpolate
-from .lacosmicpad import lacosmicpad
-from .mergemasks import merge_peak_tail_masks