teareduce 0.6.0__tar.gz → 0.6.2__tar.gz

{teareduce-0.6.0/src/teareduce.egg-info → teareduce-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.6.0
+Version: 0.6.2
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later
@@ -51,7 +51,7 @@ practical for use in Master’s level classes.
 ## Documentation
 
 The documentation for this package is available at [this
-link](https://guaix.fis.ucm.es/~tea/teareduce-cookbook/_build/html/intro.html).
+link](https://nicocardiel.github.io/teareduce-cookbook/intro.html).
 It includes Juypter notebooks that can be easily downloaded and demonstrate the
 practical use of the defined functionality.
 

{teareduce-0.6.0 → teareduce-0.6.2}/README.md

@@ -14,7 +14,7 @@ practical for use in Master’s level classes.
 ## Documentation
 
 The documentation for this package is available at [this
-link](https://guaix.fis.ucm.es/~tea/teareduce-cookbook/_build/html/intro.html).
+link](https://nicocardiel.github.io/teareduce-cookbook/intro.html).
 It includes Juypter notebooks that can be easily downloaded and demonstrate the
 practical use of the defined functionality.
 

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/cosmicraycleanerapp.py

@@ -285,17 +285,21 @@ class CosmicRayCleanerApp(ImageDisplay):
                 sdum = str(num_cr_pixels_after_dilation)
             else:
                 sdum = str(num_cr_pixels_before_dilation)
-            print("Number of cosmic ray pixels detected..........: " f"{num_cr_pixels_before_dilation:>{len(sdum)}}")
             if dilation > 0:
                 print(
-                    f"Number of cosmic ray pixels after dilation....: " f"{num_cr_pixels_after_dilation:>{len(sdum)}}"
+                    "Number of cosmic ray pixels before dilation.......: "
+                    f"{num_cr_pixels_before_dilation:>{len(sdum)}}"
+                )
+                print(
+                    f"Number of cosmic ray pixels after dilation........: "
+                    f"{num_cr_pixels_after_dilation:>{len(sdum)}}"
                 )
             # Label connected components in the mask; note that by default,
             # structure is a cross [0,1,0;1,1,1;0,1,0], but we want to consider
             # diagonal connections too, so we define a 3x3 square.
             structure = [[1, 1, 1], [1, 1, 1], [1, 1, 1]]
             self.cr_labels, self.num_features = ndimage.label(self.mask_crfound, structure=structure)
-            print(f"Number of cosmic ray features (grouped pixels): {self.num_features:>{len(sdum)}}")
+            print(f"Number of cosmic ray features (grouped pixels)....: {self.num_features:>{len(sdum)}}")
             self.replace_detected_cr_button.config(state=tk.NORMAL)
             self.review_detected_cr_button.config(state=tk.NORMAL)
             self.update_cr_overlay()
@@ -886,10 +890,7 @@ class CosmicRayCleanerApp(ImageDisplay):
                 mask_crfound2 = mask_crfound2 & (usefulmask.astype(bool))
                 # Combine results from both runs
                 if np.any(mask_crfound):
-                    print(f"Number of cosmic ray pixels (run1).......: {np.sum(mask_crfound)}")
-                    print(f"Number of cosmic ray pixels (run2).......: {np.sum(mask_crfound2)}")
-                    mask_crfound = merge_peak_tail_masks(mask_crfound, mask_crfound2)
-                    print(f"Number of cosmic ray pixels (run1 & run2): {np.sum(mask_crfound)}")
+                    mask_crfound = merge_peak_tail_masks(mask_crfound, mask_crfound2, verbose=True)
                 # Use the cleandata from the second run
                 cleandata_lacosmic = cleandata_lacosmic2
             # Select the image region to process
@@ -936,9 +937,6 @@ class CosmicRayCleanerApp(ImageDisplay):
             # recalculate labels and number of features
             structure = [[1, 1, 1], [1, 1, 1], [1, 1, 1]]
             self.cr_labels, self.num_features = ndimage.label(self.mask_crfound, structure=structure)
-            sdum = str(np.sum(self.mask_crfound))
-            print(f"Number of cosmic ray pixels detected by L.A.Cosmic...........: {sdum}")
-            print(f"Number of cosmic rays (grouped pixels) detected by L.A.Cosmic: {self.num_features:>{len(sdum)}}")
             # Define parameters for L.A.Cosmic from default dictionary
             editor_window = tk.Toplevel(self.root)
             center_on_parent(child=editor_window, parent=self.root)

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/imagedisplay.py

@@ -11,6 +11,7 @@
 
 from tkinter import simpledialog
 import numpy as np
+from rich import print
 
 from ..sliceregion import SliceRegion2D
 from ..zscale import zscale

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/interpolate.py

@@ -18,8 +18,9 @@ except ModuleNotFoundError as e:
         "`pip install teareduce[cleanest]`."
     ) from e
 import numpy as np
+from rich import print
 from scipy import ndimage
-from tqdm import tqdm
+from tqdm.notebook import tqdm
 
 from .dilatemask import dilatemask
 from .interpolation_x import interpolation_x
@@ -33,6 +34,19 @@ def interpolate(data, mask_crfound, dilation=0, interp_method=None, npoints=None
     The original data and mask are not modified. A copy of both
     arrays are created and returned with the interpolated pixels.
 
+    Cosmic-ray pixels are initially dilated by the specified number
+    of pixels. The resulting flagged pixels are grouped into cosmic-ray
+    features. Each cosmic-ray feature is then interpolated using the
+    specified interpolation method.
+
+    Note that the interpolation methods `lacosmic` and `auxfile`,
+    available in the interactive use of **tea-cleanest** are not
+    implemented in this function because both cases are simply
+    an inmediate replacement of the cosmic ray pixels in the data
+    array by the corresponding pixels in another array using the
+    mask array. Therefore, these two methods do not require any
+    interpolation algorithm.
+
     Parameters
     ----------
     data : 2D numpy.ndarray
@@ -111,7 +125,7 @@ def interpolate(data, mask_crfound, dilation=0, interp_method=None, npoints=None
         num_cr_cleaned = num_features
     elif interp_method in ["x", "y", "s", "d", "m"]:
         num_cr_cleaned = 0
-        for cr_index in tqdm(range(1, num_features + 1), disable=not debug):
+        for cr_index in tqdm(range(1, num_features + 1), disable=not debug, leave=True):
             if interp_method in ["x", "y"]:
                 if 2 * npoints <= degree:
                     raise ValueError("2*npoints must be greater than degree for polynomial interpolation.")

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/interpolation_a.py

@@ -10,6 +10,7 @@
 """Surface interpolation (plane fit) or median interpolation"""
 
 import numpy as np
+from rich import print
 
 from .dilatemask import dilatemask
 

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/interpolation_x.py

@@ -10,6 +10,7 @@
 """Polynomial nterpolation in the X direction"""
 
 import numpy as np
+from rich import print
 
 
 def interpolation_x(data, mask_fixed, cr_labels, cr_index, npoints, degree):

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/interpolation_y.py

@@ -10,6 +10,7 @@
 """Polynomial nterpolation in the Y direction"""
 
 import numpy as np
+from rich import print
 
 
 def interpolation_y(data, mask_fixed, cr_labels, cr_index, npoints, degree):

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/interpolationeditor.py

@@ -13,6 +13,8 @@ import tkinter as tk
 from tkinter import messagebox
 from tkinter import ttk
 
+from rich import print
+
 from .centerchildparent import center_on_parent
 from .definitions import VALID_CLEANING_METHODS
 from .definitions import MASKFILL_OPERATOR_VALUES
@@ -423,7 +425,7 @@ class InterpolationEditor:
     def action_on_method_change(self):
         """Handle changes in the selected cleaning method."""
         selected_method = self.cleaning_method_var.get()
-        print(f"Selected cleaning method: {selected_method}")
+        print(f"Selected cleaning method: [red bold]{selected_method}[/red bold]")
         if selected_method in ["x interp.", "y interp."]:
             self.entry_npoints.config(state="normal")
             self.entry_degree.config(state="normal")

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/lacosmicpad.py

@@ -18,6 +18,7 @@ except ModuleNotFoundError as e:
         "`pip install teareduce[cleanest]`."
     ) from e
 import numpy as np
+from rich import print
 
 from .definitions import VALID_LACOSMIC_PSFMODEL_VALUES
 from .gausskernel2d_elliptical import gausskernel2d_elliptical
@@ -28,7 +29,8 @@ def lacosmicpad(pad_width, show_arguments=False, **kwargs):
 
     This function pads the input image array before applying the LACosmic
     cosmic ray cleaning algorithm. After processing, the padding is removed
-    to return an array of the original size.
+    to return an array of the original size. If `inbkg` or `invar` arrays
+    are provided, they are also padded accordingly.
 
     The padding helps to mitigate edge effects that can occur during the
     cosmic ray detection and cleaning process.

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/cleanest/mergemasks.py

@@ -11,9 +11,10 @@
 
 import numpy as np
 from scipy import ndimage
+from rich import print
 
 
-def merge_peak_tail_masks(mask_peaks, mask_tails):
+def merge_peak_tail_masks(mask_peaks, mask_tails, verbose=False):
     """Merge peak and tail masks for cosmic ray cleaning.
 
     Tail pixels are preserved only if they correspond to CR features
@@ -25,6 +26,8 @@ def merge_peak_tail_masks(mask_peaks, mask_tails):
         Boolean array indicating the pixels identified as cosmic ray peaks.
     mask_tails : ndarray
         Boolean array indicating the pixels identified as cosmic ray tails.
+    verbose: bool
+        If True, print additional information during processing.
 
     Returns
     -------
@@ -41,6 +44,10 @@ def merge_peak_tail_masks(mask_peaks, mask_tails):
     if mask_peaks.dtype != bool or mask_tails.dtype != bool:
         raise TypeError("Input masks must be boolean arrays.")
 
+    if verbose:
+        ndigits = np.max([len(str(np.sum(mask_peaks))), len(str(np.sum(mask_tails)))])
+        print(f"Number of cosmic ray pixels (peaks)...............: {np.sum(mask_peaks):{ndigits}d}")
+        print(f"Number of cosmic ray pixels (tails)...............: {np.sum(mask_tails):{ndigits}d}")
     # find structures in tail mask
     structure = [[1, 1, 1], [1, 1, 1], [1, 1, 1]]
     cr_labels_tails, num_crs_tails = ndimage.label(mask_tails, structure=structure)
@@ -55,4 +62,7 @@ def merge_peak_tail_masks(mask_peaks, mask_tails):
         if icr > 0:
             merged_mask[cr_labels_tails == icr] = True
 
+    if verbose:
+        print(f"Number of cosmic ray pixels (merged peaks & tails): {np.sum(merged_mask):{ndigits}d}")
+
     return merged_mask

{teareduce-0.6.0 → teareduce-0.6.2}/src/teareduce/version.py

@@ -9,7 +9,7 @@
 #
 """Module to define the version of the teareduce package."""
 
-VERSION = '0.6.0'
+VERSION = '0.6.2'
 
 
 def main():

{teareduce-0.6.0 → teareduce-0.6.2/src/teareduce.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.6.0
+Version: 0.6.2
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later
@@ -51,7 +51,7 @@ practical for use in Master’s level classes.
 ## Documentation
 
 The documentation for this package is available at [this
-link](https://guaix.fis.ucm.es/~tea/teareduce-cookbook/_build/html/intro.html).
+link](https://nicocardiel.github.io/teareduce-cookbook/intro.html).
 It includes Juypter notebooks that can be easily downloaded and demonstrate the
 practical use of the defined functionality.