roll back to skip the rotamer and maskmer generation prior the template...

roll back to skip the rotamer and maskmer generation prior the template matching, which accelaratate the program since MPI wasn't involved in these two separated processes .

.idea/ruff.xml

 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="RuffConfigService">
-    <option name="projectRuffExecutablePath" value="$USER_HOME$/anaconda3/bin/ruff" />
+    <option name="projectRuffExecutablePath" value="$USER_HOME$/anaconda3/envs/catm/bin/ruff" />
   </component>
 </project>
\ No newline at end of file

README.md

@@ -15,7 +15,7 @@ python version at least 3.5 is required, create a separated environment if you w
 1.  Creat a new vitual enviroment (optional)
 
 ```
-conda create -n CATM python 
+conda create -n catm python 
 ```
 2. Download the package from gitlab and change directory to the CATM folder
 ```
@@ -23,7 +23,7 @@ git clone https://git.biohpc.swmed.edu/s194231/cryo-catm.git
 cd cryo-catm
 ```
 
-2.  Install the package
+2.  Install the package, if you want to build your own code activiely, add -dev option
 
 ```
 pip install .
@@ -33,7 +33,7 @@ pip install .
 
 ```
 cd test
-CATM #run the main program
+catm #run the main program
 ```
 
 

src/catm.py

@@ -45,7 +45,7 @@ def main():
     user_inputs = parse_input()
     if hasattr(config, "testTM"):  # this will run only the global TM
         if config.testTM:
-            print("Running general template matching!")
+            print("Running regular template matching!")
             matcher = TemplateMatcherGeneral(user_inputs)
             matcher.run_multiprocessing()
             end_time = time.time()
@@ -61,7 +61,7 @@ def main():
         obj_xml = matcher.run_multiprocessing()
         print("Template matching finished, saving results")
     else:
-        print("Bypassing template matching")
+        print("Bypassed template matching")
         # for debugging, read the xml file
         from lxml.etree import XMLParser, parse
 

src/global_template_matching.py

@@ -65,7 +65,6 @@ class TemplateMatcherGeneral:
             indices = list(range(len(self.global_angles)))
             results = pool.map(self.match_worker, indices)
             # Process results in order
-        print(len(results))
         print("Template matching is done, sorting the results!")
         # scores, rot_new, coord_new, model = [], [], [], []
         # Initialize the arrays
@@ -86,7 +85,6 @@ class TemplateMatcherGeneral:
             # Assign the temporary array to rot_save where the mask is True
             rot_save[mask] = temp_array[mask]
         # Verify the result for one element
-        print(rot_save[0, 0, 0])  # Example verification
         """        rot_save = np.empty(self.dims, dtype=object)
         ccc_save = np.zeros(self.dims)
         for cur_ccc, cur_rot in results:

src/template_matching.py

@@ -54,6 +54,7 @@ class TemplateMatcher:
             ctf_volumes = prepare_ctf_volumes(self.ctf, self.templates)
         else:
             ctf_volumes = []
+        #print("Working on subtomogram " + str(index))
         score, rots, coords, models = self.template_match(
             subtomo, angles, self.coords[index], ctf_volumes
         )
@@ -212,7 +213,6 @@ class TemplateMatcher:
                     mask = apply_wedge(mask, self.missing_wedge)
                     mask[mask < 0.5] = 0  # the mask should be binary
                     mask[mask >= 0.5] = 1
-
                 cur_ccc.append(calculate_correlation(subtomo[temp], template_rot, mask))
             ccc_save, rot_save, coor_save = self.get_best_match(
                 cur_ccc,