From 3bbd8a8bab1c15837eaad9c2319af909714546a0 Mon Sep 17 00:00:00 2001
From: Huabin Zhou <huabin.zhou@utsouthwestern.edu>
Date: Fri, 4 Oct 2024 14:42:10 -0500
Subject: [PATCH] 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 | 2 +-
README.md | 6 +++---
src/catm.py | 4 ++--
src/global_template_matching.py | 2 --
src/template_matching.py | 2 +-
5 files changed, 7 insertions(+), 9 deletions(-)
diff --git a/.idea/ruff.xml b/.idea/ruff.xml
index d2889cf..d3a43c2 100644
--- a/.idea/ruff.xml
+++ b/.idea/ruff.xml
@@ -1,6 +1,6 @@
<?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
diff --git a/README.md b/README.md
index 4ea2e64..4913d0c 100644
--- a/README.md
+++ b/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
```
diff --git a/src/catm.py b/src/catm.py
index 0386331..642ec8c 100644
--- a/src/catm.py
+++ b/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
diff --git a/src/global_template_matching.py b/src/global_template_matching.py
index 40d3eb0..9546403 100644
--- a/src/global_template_matching.py
+++ b/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:
diff --git a/src/template_matching.py b/src/template_matching.py
index 108c6af..4913e51 100644
--- a/src/template_matching.py
+++ b/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,
--
GitLab