fixed subtracting the bias from the flat in skyfit2. added a flag to …

…enable it if desired.

Utils/SkyFit2.py

@@ -442,7 +442,7 @@ def __len__(self):
 
 class PlateTool(QtWidgets.QMainWindow):
     def __init__(self, input_path, config, beginning_time=None, fps=None, gamma=None, use_fr_files=False, \
-        geo_points_input=None, startUI=True, mask=None, nobg=False, flipud=False):
+        geo_points_input=None, startUI=True, mask=None, nobg=False, flipud=False, flatbiassub=False):
         """ SkyFit interactive window.
 
         Arguments:
@@ -462,6 +462,7 @@ def __init__(self, input_path, config, beginning_time=None, fps=None, gamma=None
             startUI: [bool] Start the GUI. True by default.
             nobg: [bool] Do not subtract the background for photometry. False by default.
             flipud: [bool] Flip the image upside down. False by default.
+            flatbiassub: [bool] Subtract flat and bias frames. False by default.
         """
 
         super(PlateTool, self).__init__()
@@ -490,6 +491,9 @@ def __init__(self, input_path, config, beginning_time=None, fps=None, gamma=None
         # Store the flip upside down flag
         self.flipud = flipud
 
+        # Store the flat and bias subtraction flag
+        self.flatbiassub = flatbiassub
+
         # Extract the directory path if a file was given
         if os.path.isfile(self.dir_path):
             self.dir_path, _ = os.path.split(self.dir_path)
@@ -2762,6 +2766,10 @@ def loadState(self, dir_path, state_name, beginning_time=None, mask=None):
         if not hasattr(self, "flipud"):
             self.flipud = False
 
+        # Update the possibly missing flag for subtracting the bias from the flat
+        if not hasattr(self, "flatbiassub"):
+            self.flatbiassub = False
+
         # If the paired stars are a list (old version), reset it to a new version where it's an object
         if isinstance(self.paired_stars, list):
 
@@ -3110,8 +3118,8 @@ def keyPressEvent(self, event):
             # Set focus back on the SkyFit window
             self.activateWindow()
 
-            # Apply the dark to the flat
-            if self.flat_struct is not None:
+            # Apply the dark to the flat if the flatbiassub flag is set
+            if self.flatbiassub and (self.flat_struct is not None):
 
                 self.flat_struct.applyDark(self.dark)
 
@@ -6524,6 +6532,9 @@ def getVisibleUnmarkedStarsAndDistanceToMarked(marked_x_list, marked_y_list, min
 
     arg_parser.add_argument('-m', '--mask', metavar='MASK_PATH', type=str,
                             help="Path to a mask file which will be applied to the star catalog")
+
+    arg_parser.add_argument('--flatbiassub', action="store_true", \
+        help="Subtract the bias from the flat. False by default.")
 
 
 
@@ -6624,7 +6635,7 @@ def getVisibleUnmarkedStarsAndDistanceToMarked(marked_x_list, marked_y_list, min
         # Init SkyFit
         plate_tool = PlateTool(input_path, config, beginning_time=beginning_time, fps=cml_args.fps, \
             gamma=cml_args.gamma, use_fr_files=cml_args.fr, geo_points_input=cml_args.geopoints,
-            mask=mask, nobg=cml_args.nobg, flipud=cml_args.flipud)
+            mask=mask, nobg=cml_args.nobg, flipud=cml_args.flipud, flatbiassub=cml_args.flatbiassub)
 
 
     # Run the GUI app