Update cmos

FoGSE/collections/CMOSQLCollection.py

@@ -132,15 +132,26 @@ def det_ql_arcminutes():
 
 def get_cmos1_ql_ave_background():
     """ Return the dark QL frame for CMOS 1. """
-    cmos1_ql_arr = np.load(DARK_FRAME_DIR+"cmos1-ql-bkg-from-mar23-run12.npy")
+    cmos1_ql_arr = np.load(DARK_FRAME_DIR+"cmos1-ql-bkg-from-mar20-run16.npy")
     cmos1_ql_arr[0,:4] = np.min(cmos1_ql_arr[0])
     return cmos1_ql_arr
 
 def get_cmos2_ql_ave_background():
     """ Return the dark QL frame for CMOS 2. """
-    cmos2_ql_arr = np.load(DARK_FRAME_DIR+"cmos2-ql-bkg-from-mar23-run13.npy")
+    cmos2_ql_arr = np.load(DARK_FRAME_DIR+"cmos2-ql-bkg-from-mar20-run16.npy")
     cmos2_ql_arr[0,:4] = np.min(cmos2_ql_arr[0])
     return cmos2_ql_arr
 
 CMOS1_QL_AVE_BACKGROUND = get_cmos1_ql_ave_background()
-CMOS2_QL_AVE_BACKGROUND = get_cmos2_ql_ave_background()
+CMOS2_QL_AVE_BACKGROUND = get_cmos2_ql_ave_background()
+
+def get_cmos_ql_mask():
+    """ 
+    Return the QL frame mask for both CMOS  QL images to mask the bright 
+    feature found in hotter CMOS QL images. 
+    """
+    cmos_ql_mask_arr = np.ones((480, 512))
+    cmos_ql_mask_arr[0:128,0:50] = 0
+    return cmos_ql_mask_arr
+
+CMOS_QL_MASK_ARRAY = get_cmos_ql_mask()

FoGSE/windows/CMOSPCWindow.py

@@ -116,16 +116,20 @@ def update_product(self, product):
     def image_setup(self):
         """ Sets up the class for an image product. """
 
+        self.threshold = 60
+
         self.base_2d_image_settings()
 
-        self.min_val, self.max_val = 0, 1024
+        self.min_val, self.max_val = 0, 4095
 
         self.detw, self.deth = 768, 384
         self.base_update_aspect(aspect_ratio=self.detw/self.deth)
         self.graphPane = Image(imshow={"data_matrix":np.zeros((self.deth, self.detw))}, 
                                rotation=self.image_angle, 
                                keep_aspect=True,
-                               custom_plotting_kwargs={"aspect":self.aspect_ratio,
+                               custom_plotting_kwargs={"vmin":0,
+                                                       "vmax":1,
+                                                       "aspect":self.aspect_ratio,
                                                        "extent":det_pc_arcminutes()},
                                 figure_kwargs={"facecolor":(0.612, 0.671, 0.737, 1)})
         self.add_rotate_frame(alpha=0.3)
@@ -223,6 +227,9 @@ def process_image_data(self):
         uf = copy(self.my_array)
         uf[uf>self.max_val] = self.max_val
 
+        uf[:,:,self.channel[self.image_colour]][uf[:,:,self.channel[self.image_colour]]<self.threshold] = 0
+        uf[:,:,self.channel[self.image_colour]][uf[:,:,self.channel[self.image_colour]]>=self.threshold] = 1
+
         # allow this all to be looked at if need be
         return uf
 

FoGSE/windows/CMOSQLWindow.py

@@ -2,16 +2,16 @@
 A demo to walk through a CMOS QL raw file.
 """
 from copy import copy
+from matplotlib.colors import LogNorm, Normalize, LinearSegmentedColormap
 import numpy as np
 
 from PyQt6.QtWidgets import QApplication, QWidget, QGridLayout
 
-from FoGSE.collections.CMOSQLCollection import det_ql_arcminutes
+from FoGSE.collections.CMOSQLCollection import det_ql_arcminutes, CMOS_QL_MASK_ARRAY
 from FoGSE.readers.CMOSQLReader import CMOSQLReader
 from FoGSE.windows.base_windows.BaseWindow import BaseWindow
 from FoGSE.windows.base_windows.ImageWindow import Image
 
-
 class CMOSQLWindow(BaseWindow):
     """
     An individual window to display CMOS data read from a file.
@@ -118,15 +118,20 @@ def image_setup(self):
 
         self.base_2d_image_settings()
 
-        self.min_val, self.max_val = 0, 1024
+        self.min_val, self.max_val = 0, 4095
 
         self.detw, self.deth = 512, 480
         self.base_update_aspect(aspect_ratio=self.detw/self.deth)
+        cmap = LinearSegmentedColormap.from_list("cmos", ("black", "white"), N=255)
+        # vmin needs to be <=vmax
+        norm = LogNorm(vmin=1e-2, vmax=1) if "cmos1" in self.name else Normalize(vmin=1e-2, vmax=1)
         self.graphPane = Image(imshow={"data_matrix":np.zeros((self.deth, self.detw))}, 
                                rotation=self.image_angle, 
                                keep_aspect=True,
                                custom_plotting_kwargs={"aspect":self.aspect_ratio,
-                                                       "extent":det_ql_arcminutes()},
+                                                       "extent":det_ql_arcminutes(),
+                                                       "norm":norm,
+                                                       "cmap":cmap},
                                 figure_kwargs={"facecolor":(0.612, 0.671, 0.737, 1)})
         self.add_rotate_frame(alpha=0.3)
 
@@ -155,7 +160,17 @@ def image_update(self):
         # define self.qImageDetails for this particular image product
         new_im = self.process_image_data()
 
-        self.graphPane.add_plot_data(new_im)
+        _new_im = new_im[:,:,self.channel[self.image_colour]]
+        if "cmos1" in self.name:
+            vmin = np.min(_new_im[_new_im>0])
+            _new_im[_new_im<vmin] = vmin
+        else: 
+            vmin = 0
+        vmax = np.quantile(_new_im, 0.99998)
+
+        self.graphPane.im_obj.set_clim(vmin=vmin, vmax=vmax)
+
+        self.graphPane.add_plot_data(_new_im)
 
         self.my_array[:,:,self.channel[self.image_colour]] += self.ave_background_frame
 
@@ -260,6 +275,8 @@ def process_image_data(self):
         uf = copy(self.my_array)#/norm
         uf[uf>self.max_val] = self.max_val
 
+        uf[:,:,self.channel[self.image_colour]] *= CMOS_QL_MASK_ARRAY
+
         # allow this all to be looked at if need be
         return uf