teareduce 0.4.4__tar.gz → 0.4.6__tar.gz

{teareduce-0.4.4/src/teareduce.egg-info → teareduce-0.4.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.4
+Version: 0.4.6
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later

{teareduce-0.4.4 → teareduce-0.4.6}/pyproject.toml

@@ -46,6 +46,9 @@ test = [
 Homepage = "https://github.com/nicocardiel/teareduce"
 Repository = "https://github.com/nicocardiel/teareduce.git"
 
+[project.scripts]
+tea-cleanest = "teareduce.cleanest:main"
+
 [tool.setuptools.dynamic]
 version = {attr = "teareduce.version.VERSION"}
 

teareduce-0.4.6/src/teareduce/cleanest.py

@@ -0,0 +1,694 @@
+#
+# 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
+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
+
+import matplotlib
+matplotlib.use("TkAgg")
+
+
+class ReviewCosmicRay():
+    """Class to review suspected cosmic ray pixels."""
+
+    def __init__(self, root, data, mask_fixed, mask_crfound):
+        """Initialize the review window.
+
+        Parameters
+        ----------
+        root : tk.Tk
+            The main Tkinter window.
+        data : 2D numpy array
+            The original image data.
+        mask_fixed : 2D numpy array
+            Mask of previously corrected pixels.
+        mask_crfound : 2D numpy array
+            Mask of new pixels identified as cosmic rays.
+        """
+        self.root = root
+        self.data = data
+        self.data_original = data.copy()
+        self.mask_fixed = mask_fixed
+        self.mask_crfound = mask_crfound
+        self.first_plot = True
+        self.degree = 1    # Degree of polynomial for interpolation
+        self.npoints = 2   # Number of points at each side of the CR pixel for interpolation
+        # 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)
+        # Make a copy of the original labels to allow pixel re-marking
+        self.cr_labels_original = self.cr_labels.copy()
+        print(f"Number of cosmic ray pixels detected: {np.sum(self.mask_crfound)}")
+        print(f"Number of cosmic rays detected: {self.num_features}")
+        if self.num_features == 0:
+            print('No CR hits found!')
+        else:
+            self.cr_index = 1
+            self.create_widgets()
+
+    def create_widgets(self):
+        self.review_window = tk.Toplevel(self.root)
+        self.review_window.title("Review Cosmic Rays")
+        self.review_window.geometry("800x700+100+100")
+
+        self.button_frame1 = tk.Frame(self.review_window)
+        self.button_frame1.pack(pady=5)
+        self.remove_crosses_button = tk.Button(self.button_frame1, text="remove all X's", command=self.remove_crosses)
+        self.remove_crosses_button.pack(side=tk.LEFT, padx=5)
+        self.restore_cr_button = tk.Button(self.button_frame1, text="[r]estore CR", command=self.restore_cr)
+        self.restore_cr_button.pack(side=tk.LEFT, padx=5)
+        self.restore_cr_button.config(state=tk.DISABLED)
+        self.next_button = tk.Button(self.button_frame1, text="[c]ontinue", command=self.continue_cr)
+        self.next_button.pack(side=tk.LEFT, padx=5)
+
+        self.button_frame2 = tk.Frame(self.review_window)
+        self.button_frame2.pack(pady=5)
+        self.ndeg_label = tk.Button(self.button_frame2, text=f"deg={self.degree}, n={self.npoints}",
+                                    command=self.set_ndeg)
+        self.ndeg_label.pack(side=tk.LEFT, padx=5)
+        self.interp_x_button = tk.Button(self.button_frame2, text="[x] interp.", command=self.interp_x)
+        self.interp_x_button.pack(side=tk.LEFT, padx=5)
+        self.interp_y_button = tk.Button(self.button_frame2, text="[y] interp.", command=self.interp_y)
+        self.interp_y_button.pack(side=tk.LEFT, padx=5)
+        self.interp_s_button = tk.Button(self.button_frame2, text="[s] interp.", command=self.interp_s)
+        self.interp_s_button.pack(side=tk.LEFT, padx=5)
+
+        self.button_frame3 = tk.Frame(self.review_window)
+        self.button_frame3.pack(pady=5)
+        vmin, vmax = zscale(self.data)
+        self.vmin_button = tk.Button(self.button_frame3, 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_frame3, text=f"vmax: {vmax:.2f}", command=self.set_vmax)
+        self.vmax_button.pack(side=tk.LEFT, padx=5)
+        self.set_minmax_button = tk.Button(self.button_frame3, text="minmax [,]", command=self.set_minmax)
+        self.set_minmax_button.pack(side=tk.LEFT, padx=5)
+        self.set_zscale_button = tk.Button(self.button_frame3, text="zscale [/]", command=self.set_zscale)
+        self.set_zscale_button.pack(side=tk.LEFT, padx=5)
+        self.exit_button = tk.Button(self.button_frame3, text="[e]xit review", command=self.exit_review)
+        self.exit_button.pack(side=tk.LEFT, padx=5)
+
+        self.fig, self.ax = plt.subplots(figsize=(8, 5))
+        self.canvas = FigureCanvasTkAgg(self.fig, master=self.review_window)
+        # 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)
+        self.canvas_widget = self.canvas.get_tk_widget()
+        self.canvas_widget.pack(fill=tk.BOTH, expand=True)
+
+        # Matplotlib toolbar
+        self.toolbar_frame = tk.Frame(self.review_window)
+        self.toolbar_frame.pack(fill=tk.X, expand=False, pady=5)
+        self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbar_frame)
+        self.toolbar.update()
+
+        self.update_display()
+
+        self.root.wait_window(self.review_window)
+
+    def update_display(self):
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        ycr_list_original, xcr_list_original = np.where(self.cr_labels_original == self.cr_index)
+        if self.first_plot:
+            print(f"Cosmic ray {self.cr_index}: "
+                  f"Number of pixels = {len(xcr_list)}, "
+                  f"Centroid = ({np.mean(xcr_list):.2f}, {np.mean(ycr_list):.2f})")
+        # Use original positions to define the region to display in order
+        # to avoid image shifts when some pixels are unmarked or new ones are marked
+        i0 = int(np.mean(ycr_list_original) + 0.5)
+        j0 = int(np.mean(xcr_list_original) + 0.5)
+        jmin = j0 - 15 if j0 - 15 >= 0 else 0
+        jmax = j0 + 15 if j0 + 15 < self.data.shape[1] else self.data.shape[1] - 1
+        imin = i0 - 15 if i0 - 15 >= 0 else 0
+        imax = i0 + 15 if i0 + 15 < self.data.shape[0] else self.data.shape[0] - 1
+        self.region = SliceRegion2D(f'[{jmin+1}:{jmax+1}, {imin+1}:{imax+1}]', mode='fits').python
+        self.ax.clear()
+        vmin = self.get_vmin()
+        vmax = self.get_vmax()
+        xlabel = 'X pixel (from 1 to NAXIS1)'
+        ylabel = 'Y pixel (from 1 to NAXIS2)'
+        self.image_review, _, _ = imshow(self.fig, self.ax, self.data[self.region], colorbar=False,
+                                         xlabel=xlabel, ylabel=ylabel,
+                                         vmin=vmin, vmax=vmax)
+        self.image_review.set_extent([jmin + 0.5, jmax + 1.5, imin + 0.5, imax + 1.5])
+        xlim = self.ax.get_xlim()
+        ylim = self.ax.get_ylim()
+        for xcr, ycr in zip(xcr_list, ycr_list):
+            xcr += 1  # from index to pixel
+            ycr += 1  # from index to pixel
+            self.ax.plot([xcr - 0.5, xcr + 0.5], [ycr + 0.5, ycr - 0.5], 'r-')
+            self.ax.plot([xcr - 0.5, xcr + 0.5], [ycr - 0.5, ycr + 0.5], 'r-')
+        self.ax.set_xlim(xlim)
+        self.ax.set_ylim(ylim)
+        self.ax.set_title(f"Cosmic ray #{self.cr_index}/{self.num_features}")
+        if self.first_plot:
+            self.first_plot = False
+            self.fig.tight_layout()
+        self.canvas.draw()
+
+    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_review.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_review.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 set_minmax(self):
+        vmin_new = np.min(self.data[self.region])
+        vmax_new = np.max(self.data[self.region])
+        self.vmin_button.config(text=f"vmin: {vmin_new:.2f}")
+        self.vmax_button.config(text=f"vmax: {vmax_new:.2f}")
+        self.image_review.set_clim(vmin=vmin_new)
+        self.image_review.set_clim(vmax=vmax_new)
+        self.canvas.draw()
+
+    def set_zscale(self):
+        vmin_new, vmax_new = zscale(self.data[self.region])
+        self.vmin_button.config(text=f"vmin: {vmin_new:.2f}")
+        self.vmax_button.config(text=f"vmax: {vmax_new:.2f}")
+        self.image_review.set_clim(vmin=vmin_new)
+        self.image_review.set_clim(vmax=vmax_new)
+        self.canvas.draw()
+
+    def set_ndeg(self):
+        new_degree = simpledialog.askinteger("Set degree", "Enter new degree (min=0):",
+                                             initialvalue=self.degree, minvalue=0)
+        if new_degree is None:
+            return
+        new_npoints = simpledialog.askinteger("Set n", f"Enter new n (min={2*new_degree}):",
+                                              initialvalue=self.npoints, minvalue=2*new_degree)
+        if new_npoints is None:
+            return
+        self.degree = new_degree
+        self.npoints = new_npoints
+        self.ndeg_label.config(text=f"deg={self.degree}, n={self.npoints}")
+
+    def interp_x(self):
+        print(f"X-interpolation of cosmic ray {self.cr_index}")
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        ycr_min = np.min(ycr_list)
+        ycr_max = np.max(ycr_list)
+        xfit_all = []
+        yfit_all = []
+        for ycr in range(ycr_min, ycr_max + 1):
+            xmarked = xcr_list[np.where(ycr_list == ycr)]
+            if len(xmarked) > 0:
+                jmin = np.min(xmarked)
+                jmax = np.max(xmarked)
+                # mark intermediate pixels too
+                for ix in range(jmin, jmax + 1):
+                    self.cr_labels[ycr, ix] = self.cr_index
+                xmarked = xcr_list[np.where(ycr_list == ycr)]
+                xfit = []
+                zfit = []
+                for i in range(jmin - self.npoints, jmin):
+                    if 0 <= i < self.data.shape[1]:
+                        xfit.append(i)
+                        xfit_all.append(i)
+                        yfit_all.append(ycr)
+                        zfit.append(self.data[ycr, i])
+                for i in range(jmax + 1, jmax + 1 + self.npoints):
+                    if 0 <= i < self.data.shape[1]:
+                        xfit.append(i)
+                        xfit_all.append(i)
+                        yfit_all.append(ycr)
+                        zfit.append(self.data[ycr, i])
+                if len(xfit) > self.degree:
+                    p = np.polyfit(xfit, zfit, self.degree)
+                    for i in range(jmin, jmax + 1):
+                        if 0 <= i < self.data.shape[1]:
+                            self.data[ycr, i] = np.polyval(p, i)
+                            self.mask_fixed[ycr, i] = True
+                else:
+                    print(f"Not enough points to fit at y={ycr+1}")
+                    self.update_display()
+                    return
+        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.update_display()
+        if len(xfit_all) > 0:
+            self.ax.plot(np.array(xfit_all) + 1, np.array(yfit_all) + 1, 'mo', markersize=4)  # +1: from index to pixel
+            self.canvas.draw()
+
+    def interp_y(self):
+        print(f"Y-interpolation of cosmic ray {self.cr_index}")
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        xcr_min = np.min(xcr_list)
+        xcr_max = np.max(xcr_list)
+        xfit_all = []
+        yfit_all = []
+        for xcr in range(xcr_min, xcr_max + 1):
+            ymarked = ycr_list[np.where(xcr_list == xcr)]
+            if len(ymarked) > 0:
+                imin = np.min(ymarked)
+                imax = np.max(ymarked)
+                # mark intermediate pixels too
+                for iy in range(imin, imax + 1):
+                    self.cr_labels[iy, xcr] = self.cr_index
+                ymarked = ycr_list[np.where(xcr_list == xcr)]
+                yfit = []
+                zfit = []
+                for i in range(imin - self.npoints, imin):
+                    if 0 <= i < self.data.shape[0]:
+                        yfit.append(i)
+                        yfit_all.append(i)
+                        xfit_all.append(xcr)
+                        zfit.append(self.data[i, xcr])
+                for i in range(imax + 1, imax + 1 + self.npoints):
+                    if 0 <= i < self.data.shape[0]:
+                        yfit.append(i)
+                        yfit_all.append(i)
+                        xfit_all.append(xcr)
+                        zfit.append(self.data[i, xcr])
+                if len(yfit) > self.degree:
+                    p = np.polyfit(yfit, zfit, self.degree)
+                    for i in range(imin, imax + 1):
+                        if 0 <= i < self.data.shape[1]:
+                            self.data[i, xcr] = np.polyval(p, i)
+                            self.mask_fixed[i, xcr] = True
+                else:
+                    print(f"Not enough points to fit at x={xcr+1}")
+                    self.update_display()
+                    return
+        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.update_display()
+        if len(xfit_all) > 0:
+            self.ax.plot(np.array(xfit_all) + 1, np.array(yfit_all) + 1, 'mo', markersize=4)  # +1: from index to pixel
+            self.canvas.draw()
+
+    def interp_s(self):
+        print(f"S-interpolation of cosmic ray {self.cr_index}")
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        ycr_min = np.min(ycr_list)
+        ycr_max = np.max(ycr_list)
+        xfit_all = []
+        yfit_all = []
+        zfit_all = []
+        # First do horizontal lines
+        for ycr in range(ycr_min, ycr_max + 1):
+            xmarked = xcr_list[np.where(ycr_list == ycr)]
+            if len(xmarked) > 0:
+                jmin = np.min(xmarked)
+                jmax = np.max(xmarked)
+                # mark intermediate pixels too
+                for ix in range(jmin, jmax + 1):
+                    self.cr_labels[ycr, ix] = self.cr_index
+                xmarked = xcr_list[np.where(ycr_list == ycr)]
+                for i in range(jmin - self.npoints, jmin):
+                    if 0 <= i < self.data.shape[1]:
+                        xfit_all.append(i)
+                        yfit_all.append(ycr)
+                        zfit_all.append(self.data[ycr, i])
+                for i in range(jmax + 1, jmax + 1 + self.npoints):
+                    if 0 <= i < self.data.shape[1]:
+                        xfit_all.append(i)
+                        yfit_all.append(ycr)
+                        zfit_all.append(self.data[ycr, i])
+                    xcr_min = np.min(xcr_list)
+        # Now do vertical lines
+        xcr_max = np.max(xcr_list)
+        for xcr in range(xcr_min, xcr_max + 1):
+            ymarked = ycr_list[np.where(xcr_list == xcr)]
+            if len(ymarked) > 0:
+                imin = np.min(ymarked)
+                imax = np.max(ymarked)
+                # mark intermediate pixels too
+                for iy in range(imin, imax + 1):
+                    self.cr_labels[iy, xcr] = self.cr_index
+                ymarked = ycr_list[np.where(xcr_list == xcr)]
+                for i in range(imin - self.npoints, imin):
+                    if 0 <= i < self.data.shape[0]:
+                        yfit_all.append(i)
+                        xfit_all.append(xcr)
+                        zfit_all.append(self.data[i, xcr])
+                for i in range(imax + 1, imax + 1 + self.npoints):
+                    if 0 <= i < self.data.shape[0]:
+                        yfit_all.append(i)
+                        xfit_all.append(xcr)
+                        zfit_all.append(self.data[i, xcr])
+        if len(xfit_all) > 3:
+            # Construct the design matrix for a 2D polynomial fit to a plane,
+            # where each row corresponds to a point (x, y, z) and the model
+            # is z = C[0]*x + C[1]*y + C[2]
+            A = np.c_[xfit_all, yfit_all, np.ones(len(xfit_all))]
+            # Least squares polynomial fit
+            C, _, _, _ = np.linalg.lstsq(A, zfit_all, rcond=None)
+            # recompute all CR pixels to take into account "holes" between marked pixels
+            ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+            for iy, ix in zip(ycr_list, xcr_list):
+                self.data[iy, ix] = C[0] * ix + C[1] * iy + C[2]
+                self.mask_fixed[iy, ix] = True
+        else:
+            print("Not enough points to fit a plane")
+            self.update_display()
+            return
+        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.update_display()
+        if len(xfit_all) > 0:
+            self.ax.plot(np.array(xfit_all) + 1, np.array(yfit_all) + 1, 'mo', markersize=4)  # +1: from index to pixel
+            self.canvas.draw()
+
+    def remove_crosses(self):
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        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.update_display()
+
+    def restore_cr(self):
+        ycr_list, xcr_list = np.where(self.cr_labels == self.cr_index)
+        for iy, ix in zip(ycr_list, xcr_list):
+            self.data[iy, ix] = self.data_original[iy, ix]
+            self.interp_x_button.config(state=tk.NORMAL)
+            self.interp_y_button.config(state=tk.NORMAL)
+            self.interp_s_button.config(state=tk.NORMAL)
+        print(f"Restored all pixels of cosmic ray {self.cr_index}")
+        self.remove_crosses_button.config(state=tk.NORMAL)
+        self.restore_cr_button.config(state=tk.DISABLED)
+        self.update_display()
+
+    def continue_cr(self):
+        self.cr_index += 1
+        if self.cr_index > self.num_features:
+            self.cr_index = 1
+        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.update_display()
+
+    def exit_review(self):
+        self.review_window.destroy()
+
+    def on_key(self, event):
+        if event.key == 'q':
+            pass  # Ignore the "q" key to prevent closing the window
+        elif event.key == 'r':
+            if self.restore_cr_button.cget("state") != "disabled":
+                self.restore_cr()
+        elif event.key == 'x':
+            if self.interp_x_button.cget("state") != "disabled":
+                self.interp_x()
+        elif event.key == 'y':
+            if self.interp_y_button.cget("state") != "disabled":
+                self.interp_y()
+        elif event.key == 's':
+            if self.interp_s_button.cget("state") != "disabled":
+                self.interp_s()
+        elif event.key == 'right' or event.key == 'c':
+            self.continue_cr()
+        elif event.key == ',':
+            self.set_minmax()
+        elif event.key == '/':
+            self.set_zscale()
+        elif event.key == 'e':
+            self.exit_review()
+        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})")
+            ix = int(x+0.5) - 1  # from pixel to index
+            iy = int(y+0.5) - 1  # from pixel to index
+            if int(self.cr_labels[iy, ix]) == self.cr_index:
+                self.cr_labels[iy, ix] = 0
+                print(f"Pixel ({ix+1}, {iy+1}) unmarked as cosmic ray.")
+            else:
+                self.cr_labels[iy, ix] = self.cr_index
+                print(f"Pixel ({ix+1}, {iy+1}) 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.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.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-0.4.4 → teareduce-0.4.6}/src/teareduce/ctext.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
 #
@@ -9,8 +9,8 @@
 
 
 def ctext(s=None,
-          fg=None, 
-          bg=None, 
+          fg=None,
+          bg=None,
           under=False,
           rev=False,
           faint=False,
@@ -95,4 +95,3 @@ def ctext(s=None,
     result = f'{final_style}{s}\x1B[0m'
 
     return result
-

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/draw_rectangle.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
 #
@@ -56,11 +56,11 @@ def draw_rectangle(ax, image_data, x1, x2, y1, y2,
     ax.plot((x1, x2), (y2, y2), color, lw=1)
 
     if text:
-        ax.text((x1+x2)/2, y1+(y2-y1)/8, 
-                '{:.{prec}f}'.format(mean, prec=ndigits), 
-                ha='center', va='center', color=color, fontsize=fontsize)        
+        ax.text((x1+x2)/2, y1+(y2-y1)/8,
+                '{:.{prec}f}'.format(mean, prec=ndigits),
+                ha='center', va='center', color=color, fontsize=fontsize)
         ax.text((x1+x2)/2, y2-(y2-y1)/8,
-                '{:.{prec}f}'.format(std, prec=ndigits), 
+                '{:.{prec}f}'.format(std, prec=ndigits),
                 ha='center', va='top', color=color, fontsize=fontsize)
 
     return mean, std

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/imshow.py

@@ -30,13 +30,18 @@ def imshowme(data, **kwargs):
         Instance of Axes.
     img : matplotlib AxesImage
         Instance returned by ax.imshow()
+    cax : matplotlib.axes.Axes or None
+        Instance of Axes where the color bar is drawn, or None if
+        colorbar is False.
+    cbar : matplotlib.colorbar.Colorbar or None
+        Instance of Colorbar, or None if colorbar is False.
     """
     fig, ax = plt.subplots()
-    img = imshow(fig=fig, ax=ax, data=data, **kwargs)
-    return fig, ax, img
+    img, cax, cbar = imshow(fig=fig, ax=ax, data=data, **kwargs)
+    return fig, ax, img, cax, cbar
 
 
-def imshow(fig=None, ax=None, data=None,
+def imshow(fig=None, ax=None, data=None, ds9mode=False,
            crpix1=1, crval1=None, cdelt1=None, cunit1=None, cunitx=Unit('Angstrom'),
            xlabel=None, ylabel=None, title=None,
            colorbar=True, cblabel='Number of counts',
@@ -55,6 +60,10 @@ def imshow(fig=None, ax=None, data=None,
         Instance of Axes.
     data : numpy array
         2D array to be displayed.
+    ds9mode : bool
+        If True, the extent parameter is set to
+        [0.5, NAXIS1+0.5, 0.5, NAXIS2+0.5]
+        to mimic the DS9 display.
     crpix1 : astropy.units.Quantity
         Float number providing the CRPIX1 value: the reference pixel
         for which CRVAL1 is given.
@@ -85,7 +94,11 @@ def imshow(fig=None, ax=None, data=None,
     ------
     img : matplotlib AxesImage
         Instance returned by ax.imshow()
-
+    cax : matplotlib.axes.Axes or None
+        Instance of Axes where the color bar is drawn, or None if
+        colorbar is False.
+    cbar : matplotlib.colorbar.Colorbar or None
+        Instance of Colorbar, or None if colorbar is False.
     """
 
     # protections
@@ -94,13 +107,6 @@ def imshow(fig=None, ax=None, data=None,
     if not isinstance(ax, Axes):
         raise ValueError("Unexpected 'ax' argument")
 
-    # default labels
-    if xlabel is None:
-        xlabel = 'X axis (array index)'
-
-    if ylabel is None:
-        ylabel = 'Y axis (array index)'
-
     wavecalib = False
     if crpix1 is not None and crval1 is not None and cdelt1 is not None and cunit1 is not None:
         if 'extent' in kwargs:
@@ -120,11 +126,25 @@ def imshow(fig=None, ax=None, data=None,
         aspect = 'auto'
         wavecalib = True
     else:
-        if 'extent' in kwargs:
-            extent = kwargs['extent']
-            del kwargs['extent']
+        if ds9mode:
+            if 'extent' in kwargs:
+                raise ValueError('extent parameter can not be used with ds9mode=True')
+            naxis2, naxis1 = data.shape
+            extent = [0.5, naxis1 + 0.5, 0.5, naxis2 + 0.5]
+            if xlabel is None:
+                xlabel = 'X pixel (from 1 to NAXIS1)'
+            if ylabel is None:
+                ylabel = 'Y pixel (from 1 to NAXIS2)'
         else:
-            extent = None
+            if xlabel is None:
+                xlabel = 'X axis (array index)'
+            if ylabel is None:
+                ylabel = 'Y axis (array index)'
+            if 'extent' in kwargs:
+                extent = kwargs['extent']
+                del kwargs['extent']
+            else:
+                extent = None
         if 'aspect' in kwargs:
             aspect = kwargs['aspect']
             del kwargs['aspect']
@@ -163,6 +183,9 @@ def imshow(fig=None, ax=None, data=None,
     if colorbar:
         divider = make_axes_locatable(ax)
         cax = divider.append_axes("right", size="5%", pad=0.05, axes_class=Axes)
-        fig.colorbar(img, cax=cax, label=cblabel)
+        cbar = fig.colorbar(img, cax=cax, label=cblabel)
+    else:
+        cax = None
+        cbar = None
 
-    return img
+    return img, cax, cbar

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/peaks_spectrum.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright 2015-2024 Universidad Complutense de Madrid
+# Copyright 2015-2025 Universidad Complutense de Madrid
 #
 # This file is part of teareduce
 #
@@ -58,12 +58,12 @@ def find_peaks_spectrum(sx, nwinwidth, deltaflux=0, threshold=0, debugplot=False
               'pixels will be ignored')
 
     xpeaks = []  # list to store the peaks
-    
+
     if sx_shape[0] < nwinwidth:
         print('find_peaks_spectrum> sx shape......:', sx_shape)
         print('find_peaks_spectrum> nwinwidth.....:', nwinwidth)
         raise ValueError('sx.shape < nwinwidth')
-    
+
     i = nmed
     while i < sx_shape[0] - nmed:
         if sx[i] > threshold:
@@ -93,7 +93,7 @@ def find_peaks_spectrum(sx, nwinwidth, deltaflux=0, threshold=0, debugplot=False
                 i += 1
         else:
             i += 1
-    
+
     ixpeaks = np.array(xpeaks)
 
     if debugplot:

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/sliceregion.py

@@ -8,7 +8,7 @@
 #
 """Auxiliary classes to handle slicing regions in 1D, 2D, and 3D.
 
-These classes provide a way to define and manipulate slices in a 
+These classes provide a way to define and manipulate slices in a
 consistent manner, following both FITS and Python conventions.
 """
 
@@ -16,9 +16,10 @@ import re
 
 import numpy as np
 
+
 class SliceRegion1D:
     """Store indices for slicing of 1D regions.
-    
+
     The attributes .python and .fits provide the indices following
     the Python and the FITS convention, respectively.
 

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/statsummary.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
 #
@@ -22,7 +22,7 @@ def statsummary(x=None, rm_nan=False, show=True):
     Parameters
     ----------
     x : numpy array or None
-        Input array with values which statistical properties are 
+        Input array with values which statistical properties are
         requested.
     rm_nan : bool
         If True, filter out NaN values before computing statistics.
@@ -42,9 +42,9 @@ def statsummary(x=None, rm_nan=False, show=True):
 
     # protections
     if x is None:
-        return ['npoints', 'minimum', 'maximum', 
-                'mean', 'median', 'std', 'robust_std', 
-                'percentile16', 'percentile25', 'percentile75', 'percentile84'] 
+        return ['npoints', 'minimum', 'maximum',
+                'mean', 'median', 'std', 'robust_std',
+                'percentile16', 'percentile25', 'percentile75', 'percentile84']
 
     if isinstance(x, np.ndarray):
         xx = np.copy(x.flatten())

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/version.py

@@ -9,7 +9,7 @@
 #
 """Module to define the version of the teareduce package."""
 
-VERSION = '0.4.4'
+VERSION = '0.4.6'
 
 
 def main():

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/wavecal.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright 2015-2024 Universidad Complutense de Madrid
+# Copyright 2015-2025 Universidad Complutense de Madrid
 #
 # This file is part of teareduce
 #
@@ -30,10 +30,10 @@ from .sliceregion import SliceRegion1D
 
 class TeaWaveCalibration:
     """Auxiliary class to compute and apply wavelength calibration.
-    
+
     It is assumed that the wavelength and spatial directions correspond
     to the X (array columns) and Y (array rows) axes, respectively.
-    
+
     Attributes
     ----------
     ns_window : int
@@ -44,7 +44,7 @@ class TeaWaveCalibration:
         Standard deviation for Gaussian kernel to smooth median spectrum.
         A value of 0 means that no smoothing is performed.
     nx_window : int
-        Number of pixels (spectral direction) of the window where the 
+        Number of pixels (spectral direction) of the window where the
         peaks are sought. It must be odd.
     delta_flux : float
         Minimum difference between the flux at the line center and the
@@ -293,7 +293,7 @@ class TeaWaveCalibration:
             Standard deviation for Gaussian kernel to smooth median spectrum.
             A value of 0 means that no smoothing is performed.
         nx_window : int or None
-            Number of pixels (spectral direction) of the window where the 
+            Number of pixels (spectral direction) of the window where the
             peaks are sought. It must be odd.
         delta_flux : float
             Minimum difference between the flux at the line center and the
@@ -335,7 +335,7 @@ class TeaWaveCalibration:
             self.delta_flux = delta_flux
         if method is not None:
             self.method = method
-        
+
         naxis2, naxis1 = data.shape
 
         if self._naxis1 is None:
@@ -343,7 +343,7 @@ class TeaWaveCalibration:
         else:
             if naxis1 != self._naxis1:
                 raise ValueError(f'Unexpected naxis1: {naxis1}')
-        
+
         if self._naxis2 is None:
             self._naxis2 = naxis2
         else:
@@ -363,7 +363,7 @@ class TeaWaveCalibration:
 
         # initial median spectrum
         xpeaks, ixpeaks, sp_median_smooth = self._find_peaks_scan(
-            data=data, 
+            data=data,
             ns1=ns1,
             ns2=ns2,
             plot_peaks=plot_peaks,
@@ -420,12 +420,12 @@ class TeaWaveCalibration:
                              xpeaks_reference=None,
                              ns_range=None,
                              direction='up',
-                             ns_window = None,
-                             threshold = None,
-                             sigma_smooth = None,
-                             nx_window = None,
-                             delta_flux = None,
-                             method = None,
+                             ns_window=None,
+                             threshold=None,
+                             sigma_smooth=None,
+                             nx_window=None,
+                             delta_flux=None,
+                             method=None,
                              plots=False,
                              title=None,
                              pdf_output=None,
@@ -455,7 +455,7 @@ class TeaWaveCalibration:
             Standard deviation for Gaussian kernel to smooth median spectrum.
             A value of 0 means that no smoothing is performed.
         nx_window : int or None
-            Number of pixels (spectral direction) of the window where the 
+            Number of pixels (spectral direction) of the window where the
             peaks are sought. It must be odd.
         delta_flux : float
             Minimum difference between the flux at the line center and the
@@ -540,7 +540,7 @@ class TeaWaveCalibration:
             color_previous = ['blue', 'cyan']
             fig, ax = plt.subplots(figsize=(15, 15*naxis2/naxis1))
             vmin, vmax = np.percentile(data, [5, 95])
-            img = imshow(fig, ax, data, vmin=vmin, vmax=vmax, cmap='gray', title=title, aspect='auto')
+            imshow(fig, ax, data, vmin=vmin, vmax=vmax, cmap='gray', title=title, aspect='auto')
             # display previously identified lines
             yplot = np.arange(naxis2)[self._valid_scans]
             for i in range(self._nlines_reference):
@@ -549,18 +549,17 @@ class TeaWaveCalibration:
         else:
             fig = None
             ax = None
-            img = None
 
         # search for peaks in the 2D image
         dict_xpeaks = dict()
-        for ns in tqdm(range(ns_min_fits, ns_max_fits + ns_step, ns_step), 
+        for ns in tqdm(range(ns_min_fits, ns_max_fits + ns_step, ns_step),
                        desc='Finding peaks', disable=disable_tqdm):
             ns1 = ns - self.ns_window // 2
             ns1 = max([ns1, min(ns_min_fits, ns_max_fits)])
             ns2 = ns + self.ns_window // 2
             ns2 = min([ns2, max(ns_min_fits, ns_max_fits)])
             xpeaks, ixpeaks, sp_median_smooth = self._find_peaks_scan(
-                data=data, 
+                data=data,
                 ns1=ns1,
                 ns2=ns2,
                 plot_peaks=False,
@@ -585,7 +584,7 @@ class TeaWaveCalibration:
                 xpeaks_predicted = np.median(self._xpeaks_all_lines_array[(ns1-1):ns2, :], axis=0)
             for i in range(self._nlines_reference):
                 value = xpeaks_predicted[i]
-                # if there is no peak near to the expected location 
+                # if there is no peak near to the expected location
                 # (within a distance given by self.nx_window) the line
                 # is probably weak and we need to avoid jumping into
                 # another line
@@ -661,7 +660,7 @@ class TeaWaveCalibration:
         self.peak_wavelengths = wavelengths
 
     @u.quantity_input(xpeaks=u.pixel)
-    def overplot_identified_lines(self, xpeaks, spectrum, 
+    def overplot_identified_lines(self, xpeaks, spectrum,
                                   title=None, fontsize_title=16, fontsize_wave=10,
                                   pdf_output=None, pdf_only=False):
         """Overplot identified lines
@@ -790,7 +789,7 @@ class TeaWaveCalibration:
         xfit = np.arange(self._naxis2)[self._valid_scans]
         if len(xfit) <= self.degree_cdistortion:
             raise ValueError(f'Insufficient number of points to fit a polynomial of degree {self.degree_cdistortion}')
-        for i in tqdm(range(self._nlines_reference), 
+        for i in tqdm(range(self._nlines_reference),
                       desc='Fitting C distortion', disable=disable_tqdm):
             yfit = self._xpeaks_all_lines_array[self._valid_scans, i]
             poly, yres, reject = polfit_residuals_with_sigma_rejection(
@@ -1124,11 +1123,11 @@ class TeaWaveCalibration:
                 raise ValueError('You must set plots=True to make use of pdf_output')
 
         return poly_fits_yx, residual_std_yx, \
-               poly_fits_xy, residual_std_xy, \
-               crval1_linear, cdelt1_linear, crmax1_linear
+            poly_fits_xy, residual_std_xy, \
+            crval1_linear, cdelt1_linear, crmax1_linear
 
     def fit_wavelengths(self, degree_wavecalib=None,
-                        output_filename=None, history_list=None, 
+                        output_filename=None, history_list=None,
                         plots=False, title=None,
                         pdf_output=None, pdf_only=False,
                         silent_mode=False, disable_tqdm=True):
@@ -1320,9 +1319,9 @@ class TeaWaveCalibration:
         # crval1, cdelt1, crmax1, residual_std
         fig, axarr = plt.subplots(nrows=1, ncols=5, figsize=(15, 3))
         axarr = axarr.flatten()
-        for i, item in enumerate(['_array_crval1_linear', 
+        for i, item in enumerate(['_array_crval1_linear',
                                   '_array_cdelt1_linear',
-                                  '_array_crmax1_linear', 
+                                  '_array_crmax1_linear',
                                   '_array_residual_std_wav',
                                   '_array_residual_std_pix']):
             ax = axarr[i]
@@ -1357,8 +1356,7 @@ class TeaWaveCalibration:
         nrows = int(ncoeff / npprow)
         if ncoeff % npprow != 0:
             nrows += 1
-        fig, axarr = plt.subplots(nrows=nrows, ncols=npprow, 
-                                  figsize=(figwidth, 3*nrows))
+        fig, axarr = plt.subplots(nrows=nrows, ncols=npprow, figsize=(figwidth, 3*nrows))
         axarr = axarr.flatten()
         for ax in axarr:
             ax.axis('off')
@@ -1435,7 +1433,7 @@ class TeaWaveCalibration:
 
         old_x_borders_fits = np.arange(naxis1 + 1) + 0.5  # FITS convention
 
-        for k in tqdm(range(naxis2), 
+        for k in tqdm(range(naxis2),
                       desc='Applying wavelength calibration',
                       disable=disable_tqdm):
             poly = Polynomial(self._array_poly_wav[k])
@@ -1678,4 +1676,3 @@ def apply_wavecal_ccddata(infile, wcalibfile, outfile,
             cdelt1=cdelt1,
             title=f'{title_}(UNCERT extension)'
         )
-

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce/zscale.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
 #
@@ -12,8 +12,8 @@ import numpy as np
 
 def zscale(image, factor=0.25):
     """Compute z1 and z2 cuts in a similar way to Iraf.
-    
-    If the total number of pixels is less than 10, the function simply 
+
+    If the total number of pixels is less than 10, the function simply
     returns the minimum and the maximum values.
 
     Parameters
@@ -48,5 +48,5 @@ def zscale(image, factor=0.25):
         z1 = max(z1, q000)
         z2 = q500+(zslope*npixels/2)/factor
         z2 = min(z2, q1000)
-    
+
     return z1, z2

{teareduce-0.4.4 → teareduce-0.4.6/src/teareduce.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: teareduce
-Version: 0.4.4
+Version: 0.4.6
 Summary: Utilities for astronomical data reduction
 Author-email: Nicolás Cardiel <cardiel@ucm.es>
 License: GPL-3.0-or-later

{teareduce-0.4.4 → teareduce-0.4.6}/src/teareduce.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ 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
@@ -25,6 +26,7 @@ src/teareduce/zscale.py
 src/teareduce.egg-info/PKG-INFO
 src/teareduce.egg-info/SOURCES.txt
 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/tests/__init__.py

teareduce-0.4.6/src/teareduce.egg-info/entry_points.txt

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