Merge branch 'devel' into olz_volume_consensus

Author: albertmena

CHANGELOG.md

@@ -6,7 +6,7 @@
       - tomo_calculate_landmark_residuals: to calculate residuals in TS
       - tomo_detect_misalignment_residuals: to detect misalignment from residuals in TS
       - batch_tomo_misalignment_resid_statistics: Python script to calculate statistical metrics from a set of residuals
-      - tomo_tiltseries_detect_misalignment_corr: (legacy) for calculating relative shifts between tilt images, as a prealignment strategy
+      - tomo_tiltseries_detect_misalignment_corr: (to legacy) for calculating relative shifts between tilt images, as a prealignment strategy
 
    - Programs updated
       - Particle subtraction: now generates a single stack + includes noise power estimation
@@ -35,7 +35,7 @@
         - angular_continuous_assign2_gpu: Make a continuous angular assignment with GPU
         - cuda_fourier_projection
         - predict_deep_center
-        - cl2d_clustering.py
+        - cl2d_clustering
 
    - Programs updated
       - tomogram_reconstruction:  averaging with gold standard, tigre with internal interpolation, enviroment of tigre updated

installer/constants/main.py

@@ -73,7 +73,7 @@
 # Other variables
 TAB_SIZE = 4
 SECTION_MESSAGE_LEN = 60
-TAG_BRANCH_NAME = 'v3.24.12.0-Poseidon'
+TAG_BRANCH_NAME = 'v3.25.06.0-Rhea'
 
 # File names
 CONFIG_FILE = 'xmipp.conf'

installer/constants/versions.py

@@ -28,9 +28,9 @@
 from .main import XMIPP, XMIPP_CORE, XMIPP_VIZ, XMIPP_PLUGIN
 
 # Xmipp's current versions
-LATEST_RELEASE_NUMBER = '3.24.12.0'
-LATEST_RELEASE_NAME = 'v3.24.12.0-Poseidon'
-RELEASE_DATE = '23/12/2024'
+LATEST_RELEASE_NUMBER = '3.25.06.0'
+LATEST_RELEASE_NAME = 'v3.25.06.0-Rhea'
+RELEASE_DATE = '24/06/2025'
 #####################################
 DEVEL_BRANCHNAME = 'devel'					
 MASTER_BRANCHNAME = 'master'				

src/xmipp/bindings/python/envs_DLTK/xmipp_deepEMhancer.yml

@@ -6,7 +6,7 @@ channels:
   - rsanchez1369
 dependencies:
   - python=3.10
-  - deepemhancer>=0.16 #CUDA > 10 required. Drivers nvidia >= 450.80.02
+  - deepemhancer=0.16 #CUDA > 10 required. Drivers nvidia >= 450.80.02
   - numba
   - h5py
   - libstdcxx-ng # To be compatible with scipion env

src/xmipp/libraries/reconstruction/angular_project_library.cpp

@@ -197,8 +197,9 @@ void ProgAngularProjectLibrary::project_angle_vector (int my_init, int my_end, b
     FileName fn_proj;
     int mySize;
     int numberStepsPsi = 1;
+    const auto numberOfRotTilt = my_end-my_init+1;
 
-    mySize=my_end-my_init+1;
+    mySize=numberOfRotTilt;
     if (psi_sampling < 360)
     {
         numberStepsPsi = (int) (359.99999/psi_sampling);
@@ -207,11 +208,6 @@ void ProgAngularProjectLibrary::project_angle_vector (int my_init, int my_end, b
 
     if (verbose)
         init_progress_bar(mySize);
-    int myCounter=0;
-
-    for (double mypsi=0;mypsi<360;mypsi += psi_sampling)
-	for (int i=0;i<my_init;i++)
-	    myCounter++;
 //    if (shears && XSIZE(inputVol())!=0 && VShears==NULL)
 //        VShears=new RealShearsInfo(inputVol());
     if (projType == SHEARS && XSIZE(inputVol())!=0 && Vshears==nullptr)
@@ -222,16 +218,19 @@ void ProgAngularProjectLibrary::project_angle_vector (int my_init, int my_end, b
         		                      maxFrequency,
         		                      BSplineDeg);
 
-    for (double mypsi=0;mypsi<360;mypsi += psi_sampling)
+    for (std::size_t psiIndex = 0; psiIndex < numberStepsPsi; ++psiIndex)
     {
-        for (int i=my_init;i<=my_end;i++)
+        double mypsi = psiIndex * psi_sampling;
+        for (std::size_t i = 0; i < numberOfRotTilt; ++i)
         {
+            const auto index = my_init + i;
+            const auto n = psiIndex*numberOfRotTilt + i;
             if (verbose)
-                progress_bar(i-my_init);
-
-            double psi= mypsi+ZZ(mysampling.no_redundant_sampling_points_angles[i]);
-            double tilt=      YY(mysampling.no_redundant_sampling_points_angles[i]);
-            double rot=       XX(mysampling.no_redundant_sampling_points_angles[i]);
+                progress_bar(n);
+            
+            double psi= mypsi+ZZ(mysampling.no_redundant_sampling_points_angles[index]);
+            double tilt=      YY(mysampling.no_redundant_sampling_points_angles[index]);
+            double rot=       XX(mysampling.no_redundant_sampling_points_angles[index]);
 
 //            if (shears)
 //                projectVolume(*VShears, P, Ydim, Xdim, rot,tilt,psi);
@@ -247,9 +246,10 @@ void ProgAngularProjectLibrary::project_angle_vector (int my_init, int my_end, b
 
             P.setEulerAngles(rot,tilt,psi);
             P.setDataMode(_DATA_ALL);
-            P.write(output_file,(size_t) (numberStepsPsi * i + mypsi +1),true,WRITE_REPLACE);
+            P.write(output_file, (n + 1), true, WRITE_REPLACE);
         }
     }
+
     if (verbose)
         progress_bar(mySize);
 }