teareduce 0.6.5__py3-none-any.whl → 0.6.6__py3-none-any.whl

teareduce/cleanest/definitions.py

@@ -19,11 +19,11 @@ VALID_LACOSMIC_PSFMODEL_VALUES = ["gauss", "moffat", "gaussx", "gaussy", "gaussx
 # when reading user input.
 lacosmic_default_dict = {
     # L.A.Cosmic parameters for run 1
+    "run1_gain": {"value": 1.0, "type": float, "positive": True},
+    "run1_readnoise": {"value": 6.5, "type": float, "positive": True},
     "run1_sigclip": {"value": 5.0, "type": float, "positive": True},
     "run1_sigfrac": {"value": 0.3, "type": float, "positive": True},
     "run1_objlim": {"value": 5.0, "type": float, "positive": True},
-    "run1_gain": {"value": 1.0, "type": float, "positive": True},
-    "run1_readnoise": {"value": 6.5, "type": float, "positive": True},
     "run1_satlevel": {"value": 65535, "type": float, "positive": True},
     "run1_niter": {"value": 4, "type": int, "positive": True, "intmode": "any"},
     "run1_sepmed": {"value": True, "type": bool},
@@ -40,11 +40,11 @@ lacosmic_default_dict = {
     "run1_psfbeta": {"value": 4.765, "type": float, "positive": True},
     "run1_verbose": {"value": True, "type": bool},
     # L.A.Cosmic parameters for run 2
+    "run2_gain": {"value": 1.0, "type": float, "positive": True},
+    "run2_readnoise": {"value": 6.5, "type": float, "positive": True},
     "run2_sigclip": {"value": 3.0, "type": float, "positive": True},
     "run2_sigfrac": {"value": 0.3, "type": float, "positive": True},
     "run2_objlim": {"value": 5.0, "type": float, "positive": True},
-    "run2_gain": {"value": 1.0, "type": float, "positive": True},
-    "run2_readnoise": {"value": 6.5, "type": float, "positive": True},
     "run2_satlevel": {"value": 65535, "type": float, "positive": True},
     "run2_niter": {"value": 4, "type": int, "positive": True, "intmode": "any"},
     "run2_sepmed": {"value": True, "type": bool},
@@ -72,6 +72,62 @@ lacosmic_default_dict = {
     "nruns": {"value": 1, "type": int, "positive": True, "intmode": "any"},
 }
 
+# Default parameters for PyCosmic algorithm
+pycosmic_default_dict = {
+    # PyCosmic parameters for run 1
+    "run1_gain": {"value": 1.0, "type": float, "positive": True},
+    "run1_rdnoise": {"value": 6.5, "type": float, "positive": True},
+    "run1_sigma_det": {"value": 5.0, "type": float, "positive": True},
+    "run1_rlim": {"value": 1.2, "type": float, "positive": True},
+    "run1_iterations": {"value": 5, "type": int, "positive": True, "intmode": "any"},
+    "run1_fwhm_gauss_x": {"value": 2.5, "type": float, "positive": True},
+    "run1_fwhm_gauss_y": {"value": 2.5, "type": float, "positive": True},
+    "run1_replace_box_x": {"value": 5, "type": int, "positive": True, "intmode": "odd"},
+    "run1_replace_box_y": {"value": 5, "type": int, "positive": True, "intmode": "odd"},
+    "run1_replace_error": {"value": 1e6, "type": float, "positive": True},
+    "run1_increase_radius": {"value": 0, "type": int, "positive": True},
+    "run1_bias": {"value": 0.0, "type": float},
+    "run1_verbose": {"value": True, "type": bool},
+    # PyCosmic parameters for run 2
+    "run2_gain": {"value": 1.0, "type": float, "positive": True},
+    "run2_rdnoise": {"value": 6.5, "type": float, "positive": True},
+    "run2_sigma_det": {"value": 3.0, "type": float, "positive": True},
+    "run2_rlim": {"value": 1.2, "type": float, "positive": True},
+    "run2_iterations": {"value": 5, "type": int, "positive": True, "intmode": "any"},
+    "run2_fwhm_gauss_x": {"value": 2.5, "type": float, "positive": True},
+    "run2_fwhm_gauss_y": {"value": 2.5, "type": float, "positive": True},
+    "run2_replace_box_x": {"value": 5, "type": int, "positive": True, "intmode": "odd"},
+    "run2_replace_box_y": {"value": 5, "type": int, "positive": True, "intmode": "odd"},
+    "run2_replace_error": {"value": 1e6, "type": float, "positive": True},
+    "run2_increase_radius": {"value": 0, "type": int, "positive": True},
+    "run2_bias": {"value": 0.0, "type": float},
+    "run2_verbose": {"value": True, "type": bool},
+    # Limits for the image section to process (pixels start at 1)
+    "xmin": {"value": 1, "type": int, "positive": True},
+    "xmax": {"value": None, "type": int, "positive": True},
+    "ymin": {"value": 1, "type": int, "positive": True},
+    "ymax": {"value": None, "type": int, "positive": True},
+    # Number of runs to execute PyCosmic
+    "nruns": {"value": 1, "type": int, "positive": True, "intmode": "any"},
+}
+
+# Default parameters for deepCR algorithm
+deepcr_default_dict = {
+    # Model name
+    "mask": {"value": "ACS-WFC", "type": str, "valid_values": ["ACS-WFC", "WFC3-UVIS"]},
+    # Threshold for CR probability map
+    "threshold": {"value": 0.5, "type": float, "positive": True},
+    "dilation": {"value": 0, "type": int, "positive": True},
+}
+
+# Default parameters for Cosmic-CoNN algorithm
+cosmicconn_default_dict = {
+    # Threshold for CR probability map
+    "threshold": {"value": 0.5, "type": float, "positive": True},
+    # Dilation of the mask
+    "dilation": {"value": 0, "type": int, "positive": True},
+}
+
 # Valid cleaning methods (as shown to the user and their internal codes)
 VALID_CLEANING_METHODS = {
     "x interp.": "x",
@@ -80,6 +136,8 @@ VALID_CLEANING_METHODS = {
     "median": "a-median",
     "mean": "a-mean",
     "lacosmic": "lacosmic",
+    "pycosmic": "pycosmic",
+    "deepcr": "deepcr",
     "maskfill": "maskfill",
     "auxdata": "auxdata",
 }
@@ -102,7 +160,7 @@ DEFAULT_MASKFILL_VERBOSE = False
 
 # Default Tk window size
 DEFAULT_TK_WINDOW_SIZE_X = 800
-DEFAULT_TK_WINDOW_SIZE_Y = 700
+DEFAULT_TK_WINDOW_SIZE_Y = 800
 
 # Default font settings
 DEFAULT_FONT_FAMILY = "Helvetica"

teareduce/cleanest/interpolate.py

@@ -20,7 +20,7 @@ except ModuleNotFoundError as e:
 import numpy as np
 from rich import print
 from scipy import ndimage
-from tqdm.notebook import tqdm
+from tqdm.auto import tqdm
 
 from .dilatemask import dilatemask
 from .interpolation_x import interpolation_x

teareduce/cleanest/interpolationeditor.py

@@ -35,6 +35,8 @@ class InterpolationEditor:
         last_maskfill_verbose,
         auxdata,
         cleandata_lacosmic,
+        cleandata_pycosmic,
+        cleandata_deepcr,
         xmin,
         xmax,
         ymin,
@@ -65,6 +67,10 @@ class InterpolationEditor:
             Auxiliary data for cleaning, if available.
         cleandata_lacosmic : array-like or None
             Cleaned data from L.A.Cosmic, if available.
+        cleandata_pycosmic : array-like or None
+            Cleaned data from PyCosmic, if available.
+        cleandata_deepcr : array-like or None
+            Cleaned data from DeepCR, if available.
         xmin : float
             Minimum x value of the data. From 1 to NAXIS1.
         xmax : float
@@ -97,6 +103,10 @@ class InterpolationEditor:
             Auxiliary data for cleaning, if available.
         cleandata_lacosmic : array-like or None
             Cleaned data from L.A.Cosmic, if available.
+        cleandata_pycosmic : array-like or None
+            Cleaned data from PyCosmic, if available.
+        cleandata_deepcr : array-like or None
+            Cleaned data from DeepCR, if available.
         dict_interp_methods : dict
             Mapping of interpolation method names to their codes.
         cleaning_method : str or None
@@ -127,6 +137,8 @@ class InterpolationEditor:
         self.last_dilation = last_dilation
         self.auxdata = auxdata
         self.cleandata_lacosmic = cleandata_lacosmic
+        self.cleandata_pycosmic = cleandata_pycosmic
+        self.cleandata_deepcr = cleandata_deepcr
         # Initialize parameters
         self.cleaning_method = None
         self.npoints = last_npoints
@@ -169,13 +181,22 @@ class InterpolationEditor:
         for interp_method in VALID_CLEANING_METHODS.keys():
             state = "normal"
             # Skip replace by L.A.Cosmic values if last dilation is not zero
+            # or cleandata_lacosmic is not available
             if interp_method == "lacosmic":
                 if self.last_dilation != 0:
                     state = "disabled"
                 if self.cleandata_lacosmic is None:
                     state = "disabled"
+            # Skip replace by PyCosmic values if cleandata_pycosmic is not available
+            elif interp_method == "pycosmic":
+                if self.cleandata_pycosmic is None:
+                    state = "disabled"
+            # Skip replace by DeepCR values if cleandata_deepcr is not available
+            elif interp_method == "deepcr":
+                if self.cleandata_deepcr is None:
+                    state = "disabled"
             # Skip auxdata method if auxdata is not available
-            if interp_method == "auxdata" and self.auxdata is None:
+            elif interp_method == "auxdata" and self.auxdata is None:
                 state = "disabled"
             tk.Radiobutton(
                 main_frame,
@@ -454,14 +475,7 @@ class InterpolationEditor:
             self.entry_maskfill_operator.config(state="disabled")
             self.entry_maskfill_smooth.config(state="disabled")
             self.entry_maskfill_verbose.config(state="disabled")
-        elif selected_method == "lacosmic":
-            self.entry_npoints.config(state="disabled")
-            self.entry_degree.config(state="disabled")
-            self.entry_maskfill_size.config(state="disabled")
-            self.entry_maskfill_operator.config(state="disabled")
-            self.entry_maskfill_smooth.config(state="disabled")
-            self.entry_maskfill_verbose.config(state="disabled")
-        elif selected_method == "auxdata":
+        elif selected_method in ["lacosmic", "pycosmic", "deepcr", "auxdata"]:
             self.entry_npoints.config(state="disabled")
             self.entry_degree.config(state="disabled")
             self.entry_maskfill_size.config(state="disabled")

teareduce/cleanest/lacosmicpad.py

@@ -17,6 +17,7 @@ except ModuleNotFoundError as e:
         "Please install teareduce with the 'cleanest' extra dependencies: "
         "`pip install teareduce[cleanest]`."
     ) from e
+from importlib.metadata import version
 import numpy as np
 from rich import print
 
@@ -24,7 +25,7 @@ from .definitions import VALID_LACOSMIC_PSFMODEL_VALUES
 from .gausskernel2d_elliptical import gausskernel2d_elliptical
 
 
-def lacosmicpad(pad_width, show_arguments=False, **kwargs):
+def lacosmicpad(pad_width, show_arguments=False, display_ccdproc_version=True, **kwargs):
     """Execute LACosmic algorithm on a padded array.
 
     This function pads the input image array before applying the LACosmic
@@ -46,6 +47,8 @@ def lacosmicpad(pad_width, show_arguments=False, **kwargs):
         the LACosmic algorithm.
     show_arguments : bool
         If True, display LACosmic arguments being employed.
+    display_ccdproc_version : bool
+        If True, display the version of the ccdproc package being used.
     **kwargs : dict
         Keyword arguments to be passed to the `cosmicray_lacosmic` function.
 
@@ -145,13 +148,29 @@ def lacosmicpad(pad_width, show_arguments=False, **kwargs):
         else:
             raise ValueError("The 'fsmode' keyword argument must be either 'convolve' or 'median'.")
 
+    # Apply LACosmic algorithm to the padded array
+    try:
+        version_ccdproc = version("ccdproc")
+    except Exception:
+        version_ccdproc = "unknown"
+    if display_ccdproc_version:
+        print(f"Running L.A.Cosmic implementation from ccdproc version {version_ccdproc}")
+    if kwargs["verbose"] or show_arguments:
+        end = "\n"
+    else:
+        end = ""
+    print("(please wait...) ", end=end)
     # Show LACosmic arguments if requested
     if show_arguments:
         for key, value in kwargs.items():
             print(f"LACosmic parameter: {key} = {value}")
-    # Apply LACosmic algorithm to the padded array
     cleaned_padded_array, mask_padded_array = cosmicray_lacosmic(ccd=padded_array, **kwargs)
+    print(f"Done!")
     # Remove padding
-    cleaned_array = cleaned_padded_array[pad_width:-pad_width, pad_width:-pad_width]
-    mask_array = mask_padded_array[pad_width:-pad_width, pad_width:-pad_width]
+    if pad_width == 0:
+        cleaned_array = cleaned_padded_array
+        mask_array = mask_padded_array
+    else:
+        cleaned_array = cleaned_padded_array[pad_width:-pad_width, pad_width:-pad_width]
+        mask_array = mask_padded_array[pad_width:-pad_width, pad_width:-pad_width]
     return cleaned_array, mask_array