Adding function to set pixels surrounded by NaNs to desired value.

spaceKLIP/analysistools.py

@@ -36,7 +36,7 @@
 from spaceKLIP.psf import get_offsetpsf, JWST_PSF
 from spaceKLIP.starphot import get_stellar_magnitudes, read_spec_file
 from spaceKLIP.pyklippipeline import get_pyklip_filepaths
-from spaceKLIP.utils import write_starfile
+from spaceKLIP.utils import write_starfile, set_surrounded_pixels
 
 import logging
 log = logging.getLogger(__name__)
@@ -223,15 +223,15 @@ def raw_contrast(self,
                     nanmask = np.pad(nanmask, pad)
 
                     # Upsample array to improve centering. 
-                    samp = 15 #Upsampling factor
+                    samp = 1 #Upsampling factor
                     nanmask = nanmask.repeat(samp, axis=0).repeat(samp, axis=1)
 
                     # Define rectangle edges
                     rect_width = 10*samp #pixels
                     thinrect_width = 2*samp #pixels
 
                     cent_rect = [(center[0]+pad)*samp,(center[0]+pad)*samp,
-                                    (center[1]+pad)*samp,(center[1]+pad)*samp]
+                                 (center[1]+pad)*samp,(center[1]+pad)*samp]
                     rect = [int(cent_rect[i]-(rect_width/2*(-1)**(i%2))) for i in range(4)]
                     thinrect = [int(cent_rect[i]-(thinrect_width/2*(-1)**(i%2))) for i in range(4)]
 
@@ -268,6 +268,7 @@ def raw_contrast(self,
                     # Downsample, remove padding, and mask data
                     nanmask = nanmask[::samp,::samp]
                     nanmask = nanmask[pad:-pad,pad:-pad]
+                    nanmask = set_surrounded_pixels(nanmask)
                     data *= nanmask
                 elif self.database.red[key]['EXP_TYPE'][j] in ['MIR_LYOT']:
                     raise NotImplementedError()

spaceKLIP/utils.py

@@ -618,11 +618,11 @@ def write_starfile(starfile,
     Parameters
     ----------
     starfile : str
-        Path to original stellar spectrum file
+        Path to original stellar spectrum file.
     new_starfile_path : str
-        Path to new stellar spectrum file
+        Path to new stellar spectrum file.
     new_header : str
-        Header to be inserted 
+        Header to be inserted. 
     
     Returns
     -------
@@ -639,3 +639,31 @@ def write_starfile(starfile,
                 new_starfile.write(text)
             else:
                 new_starfile.write(new_header+text)
+
+def set_surrounded_pixels(array, user_value=np.nan):
+    """
+    Identifies pixels in a 2D array surrounded by NaN values 
+    on all eight sides and sets them to a user-defined value.
+
+    Parameters
+    ----------
+    array : numpy.ndarray
+        2D array containing numeric values and NaNs.
+    user_value : float or any valid value type, optional
+        Value to set for pixels surrounded by NaNs on all eight sides. Defaults to NaN.
+
+    Returns
+    -------
+    numpy.ndarray
+        The input array with pixels surrounded by NaNs on all eight sides set to the user-defined value.
+    """
+    nan_mask = np.isnan(array)
+    surrounded_pixels = (
+        ~nan_mask[1:-1, 1:-1] &
+        nan_mask[:-2, :-2] & nan_mask[:-2, 1:-1] & nan_mask[:-2, 2:] &
+        nan_mask[1:-1, :-2] & nan_mask[1:-1, 2:] &
+        nan_mask[2:, :-2] & nan_mask[2:, 1:-1] & nan_mask[2:, 2:]
+    )
+
+    array[1:-1, 1:-1][surrounded_pixels] = user_value
+    return array