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 .

src/test/s68/catm/config.py

+# config.py
+
+import os
+"""
+The input and configureation:
+1.The tomogram, should be black on white background
+2.The templates, needs to be white on black background, to be consistent with normal convention
+3.The coordinates of picked particles
+4.The missing wedge information, default to [30,42], corresponding to [-60,+48] tilt range
+5.The shrinkage factor, default to 0.3, this controls the contours of the template
+6. There are more high level parameters, like the search depth, etc.
+"""
+
+############################ input && output control ##################################
+current_dir = os.getcwd()
+split_path = current_dir.split("/")
+tomoID = split_path[-2]
+prefix = tomoID + ".test1.catm"
+input_folder = 'inputs/'
+tomogram = input_folder +tomoID+".test1.lps25.mrc"
+
+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
+# One can create the mask in Relion with soft edges, extend 2 and soft 3 is recommended
+masks = [
+    input_folder + 'mask-mono-8Apx-lps30-box30-rot12-ex2-s2.mrc',
+]
+# Coordinates of picked particles,you might also include the angles for local search
+df = input_folder+'s68.pick1.csv'#'../cluster/s'+str(tomoID)+'.unetn_4.5.csv'
+
+# We need the missing wedge information or a CTF model
+# You might create a CTF model via Relion or Warp, which should be generic for data collected with the microscope
+# If a CTF model present, it will be use by default
+ctf_model_file = input_folder+ tomoID + "_0000000_ctf_8.00A.mrc"  # path to the CTF model
+# output path
+output_path = "results/"
+write_models = True  # Generate a volume with assigned models
+
+mpi_nn = -1 # -1 will use all the availbe cpu
+
+############################ Template Matching Control ##################################
+
+# Missing wedge information, if CTF model is not found
+missing_wedge = [30, 42]  # [30,42] Corresponding to [-60, +48] tilt range
+
+# Shrinkage factor, which the counter level of the volume, can be determined in Chimera
+# It's designed to control how close two objects are allowed to be
+# only template 1 will be used for the cleaning of clashes
+shrinkage_factor = 1
+
+# Number of angles for global template matching
+number_of_angles = 2000
+# The minimum CCCs kept after template matching
+min_CCC = 0.1
+
+# Range of local search angles, only for local search, default to False for global search
+# For local searchthe rough angles need to be provied in the coords.csv,
+# with columns phi, theta, psi in intrinsic ZXZ convention
+local_search_angles = False  # False or True
+
+# searching space
+matching_space = 3  # in pixels, how far from the original position to search
+
+############################ Clash Resolver Control ##################################
+
+# Search depth, control how many rotataions
+search_depth = 200
+
+# for development
+bypass_TM = False
+bypass_CR = False
+sort_score = True  # this is useful if you don't want to mix up the index
+
+
+############################ For Development ##################################
+pre_assigned_volume =  None #'s'+tomoID+'-pre-assigned-vol.mrc' # path to the pre-assigned volume
+bypass_optimizer = False  # this will bypass the optimizer clash resolver
+distance_tolerance = 2
+adjust_ccc = None
+# max distance between two partles to be considered as the same particle
+# option's for running only the general template matching
+testTM = False
+chunk_size = None #[304,776,776]#[152,194,194]

src/test/s68/catm/inputs/s68.pick1.csv

+x,y,z
+23,19,14
+19,22,26
+20,8,26
+12,33,34
+30,16,5

src/test/s68/catm/results/s68.test1.catm.coords

+23 18 14 101.0 91.99999999999999 121.0
+12 32 32 126.99999999999999 119.99999999999999 47.000000000000014
+17 7 25 -27.000000000000007 54.99999999999999 64.00000000000001
+29 15 3 90.99999999999999 93.0 -46.99999999999999
+18 21 25 -27.000000000000007 54.99999999999999 64.00000000000001

src/test/s68/catm/results/s68.test1.catm.csv

+x,y,z,phi,theta,psi,ccc,model
+23.0,18.0,14.0,-169.0,92.0,31.0,0.565712,0.0
+12.0,32.0,32.0,-143.0,120.0,-43.0,0.513825,0.0
+17.0,7.0,25.0,63.0,55.0,-26.0,0.444633,0.0
+29.0,15.0,3.0,-179.0,93.0,-137.0,0.46157,0.0
+18.0,21.0,25.0,63.0,55.0,-26.0,0.420571,0.0

src/test/s68/catm/results/s68.test1.catm.star

+# Created by the starfile Python package (version 0.5.1) at 14:03:30 on 04/10/2024
+
+
+data_
+
+loop_
+_rlnCoordinateX #1
+_rlnCoordinateY #2
+_rlnCoordinateZ #3
+_rlnAngleRot #4
+_rlnAngleTilt #5
+_rlnAnglePsi #6
+_ccc #7
+23	18	14	101.000000	92.000000	121.000000	0.565712
+12	32	32	127.000000	120.000000	47.000000	0.513825
+17	7	25	-27.000000	55.000000	64.000000	0.444633
+29	15	3	91.000000	93.000000	-47.000000	0.461570
+18	21	25	-27.000000	55.000000	64.000000	0.420571
+
+

src/test/s68/catm/results/s68.test1.catm.xml

+<objlist>
+  <subtomo>
+    <object subtomo_idx="0" x="23" y="18" z="14" phi="-169" theta="92" psi="31" CCC="0.565712" model="0.000000"/>
+  </subtomo>
+  <subtomo>
+    <object subtomo_idx="1" x="12" y="32" z="32" phi="-143" theta="120" psi="-43" CCC="0.513825" model="0.000000"/>
+  </subtomo>
+  <subtomo>
+    <object subtomo_idx="2" x="17" y="7" z="25" phi="63" theta="55" psi="-26" CCC="0.444633" model="0.000000"/>
+  </subtomo>
+  <subtomo>
+    <object subtomo_idx="3" x="29" y="15" z="3" phi="-179" theta="93" psi="-137" CCC="0.461570" model="0.000000"/>
+  </subtomo>
+  <subtomo>
+    <object subtomo_idx="4" x="18" y="21" z="25" phi="63" theta="55" psi="-26" CCC="0.420571" model="0.000000"/>
+  </subtomo>
+</objlist>

src/test/s68/inputs/s68.pick1.csv

+x,y,z
+23,19,14
+19,22,26
+20,8,26
+12,33,34
+30,16,5