Fixt the tomogram contrast config

src/file_handler.py

@@ -166,6 +166,7 @@ def parse_input():
     tomogram = read_mrc(user_inputs["tomogram"])
     if not user_inputs['black_on_white']:
         tomogram = -tomogram
+        print("Inverted the tomogram contrast to match template.")
     dims = tomogram.shape
     templates = [read_mrc_permissive(template) for template in user_inputs["templates"]]
     if user_inputs["masks"]:

test/s68/catm/config.py

@@ -19,7 +19,7 @@ tomoID = split_path[-2]
 prefix = tomoID + ".test1.catm"
 input_folder = "inputs/"
 tomogram = input_folder + tomoID + ".test1.lps25.mrc"
-
+black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
 templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
 contour_level = [0.2]
 #  Masks are required to be the same shape as the templates

test/s68/tm/config.py

@@ -19,6 +19,7 @@ tomoID = split_path[-2]
 prefix = tomoID + ".test1"
 input_folder = "inputs/"
 tomogram = input_folder + tomoID + ".test1.lps25.mrc"
+black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
 
 templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
 contour_level = [0.2]