scipion-em-xmipp 24.6.0.0__tar.gz → 25.6.0__tar.gz

scipion-em-xmipp-24.6.0.0/CHANGES.md → scipion_em_xmipp-25.6.0/CHANGELOG.md

@@ -1,3 +1,85 @@
+## Release 3.25.06.0 - Rhea
+- New protocols
+   - compute_likelihood: This protocol computes the likelihood of a set of particles with assigned angles when compared to a set of maps or atomic modelS
+
+- Protocols updated
+   - Max shift: tolerate movies without micrographs associated
+   - substract_projection: update command to boost and subtract to generate only one output stack
+   - Movie alignment consensus protocol: enables irregular input sets. Changes in functionality; comparisons between ons between shifts trajectories, and a additional change related to the minimum consensus or threshold for shifts correlation.
+   - volume_adjust_sub: better label for volume 1 vs 2
+   - convert_pdb: aDD binThreads
+   - align_volume: add possible
+   - particle_pick_consensus: Fixed ID mismatch when combining coordinate sets; now supports asymmetrical sets without indexing errors.
+   - movie_split_frames: now allows testing sum_frames, includes a summary, improved layout, and updated test.
+   - deep_Consensus: GPU handling
+   - Deep_hand: handling env to avoid system CUDA settings,  erasing cuda things from env['LD_LIBRARY_PATH']
+   - Extract particles protocol: force output boxsize
+   - reconstruct_fourier: correctEnvelope False by default
+   - reconstruct_highres: test updated, correctEnvelope False by default
+   - Structure map: Adding a dendrogram and removing some intermediate files
+
+
+- Protocols fixed
+   - simulate ctf: fix pre-CTF noise np.numpy, init generator for pre and post ctf noise
+   - validate FSCQ: test fixed
+   - resolution_monogenic_signal: fixing header in MonoRes
+   - protocol_process: CropResize halves fix
+   - Extract particles test fixed
+   - FSO viewer: the fso was failing when the fso did not cross some thresholds
+   - reconstruct_significant: fix gpu usage
+   - ransac: fix gpu usage
+     
+- Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols](https://i2pc.github.io/docs/Utils/Deprecated-programs/index.html)))
+   - XmippProtScreenDeepLearning
+
+- More scipion-em-xmipp
+   - Most of the Xmipp dependencies installed on Scipion env
+   - Updating version for pypi requirements
+   - Bug cloning tag
+   - Use toml for installation
+   - Bug fixed related to the WriteSetOfParticles and the Missing ExtraLabels (The Oier and Fede Adventures)
+   - Handling nvidia drivers error message
+   - improving deps installation
+   - Improved the help message of more than 60 protocols
+        
+## Release 3.24.12 - Poseidon
+   - New protocols
+      - apply_tilt_to_ctf: Apply a local deviation to the CTF based on the micrograph's tilt
+    angle
+      - mics_defocus_balancer: It takes as input a certain number of CTFs and makes a balanced sampling of N images based on the defocus U values
+      - deep_center_predict: Center a set of particles in 2D using a neural network
+      - cl2d_clustering: 2D clustering protocol to group similar images (2D Averages or 2D Classes)
+
+   - Protocols updated
+      - flexalign: Added support for reading EER. Optimized and refactor the streaming, the continue action stabilized. FlexAlign can run multiple times in a single GPU or in multiple GPUs from within Scipion3.
+      - convert_pdb: now can read cif
+      - create_gallery: Allow Scipion protocol create gallery to access missing projection options
+      - ctf_consensus: optimized and refactor the streaming, the continue action stabilized. Remove parallelization
+      - movie_dose_analysis: optimized and refactor the streaming, the continue action stabilized
+      - movie_max_shift: optimized and refactor the streaming, the continue action stabilized, Remove parallelization
+      - tilt_analysis: optimized and refactor the streaming, the continue action stabilized
+      - subtract_projection: Adaptations for new logic in Xmipp program
+      - reconstruct_highres: Add GPU use for local angle assignment 
+
+   - Protocols fixed
+      -  trigger_data: Fix the way we split the output
+      -  subtract_projection: fnMask sub
+      -  classify_pca: Bug fix in the validate function
+      -  reconstruct_fourier: Fourier reconstruction now allows performing the CTF correction inside the same protocol.
+      -  volume_local_sharpening: local deblur performs now a single iteration by defaul
+      -  movie_max_shift: fixed with several parallel threads in streaming
+      -  reconstruct_highres: add unassigned vars fnVol1 fnVol2 to set loop
+      -  ctf_defocus_group: fix when testing multiple downsampling factors
+      -  ctf_micrographs: fix when testing multiple downsampling factors
+
+   - Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols))
+      - angular_resolution_alignment
+      - movie_opticalflow.py
+        
+   - More scipion-em-xmipp
+      - scikit-learn updated to 1.2
+      - protocols.conf list completed. All protocols are listed and clustered in Scipion
+
 ## Release 3.24.06 - Oceanus
    - New protocols
       - movie_alignment_consensus: protocol for the comparison of two global alignments
@@ -28,7 +110,7 @@
       - metaprotocol_golden_highres
       - solid_angle
       - split_volume
-   - More scipio-em-xmipp
+   - More scipion-em-xmipp
       - Solve Sonar Cloud reported bugs
       - Flexible import of pyQT on chimera script
       - Removing tkAgg matplotlib requirement in viewer_structure_map
@@ -58,7 +140,7 @@
       - classification_gpuCorr
       - classification_gpuCorr_full
       - classification_gpuCorr_semi
-   - More scipio-em-xmipp
+   - More scipion-em-xmipp
       - Updated Nvidia driver required version
 
 

scipion_em_xmipp-25.6.0/PKG-INFO

@@ -0,0 +1,38 @@
+Metadata-Version: 2.1
+Name: scipion-em-xmipp
+Version: 25.6.0
+Summary: Plugin to use Xmipp programs within the Scipion framework.
+Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://github.com/I2PC/scipion-em-xmipp
+Project-URL: Issues, https://github.com/I2PC/scipion-em-xmipp/issues
+Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipion-pyworkflow>=3.0.31
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-image
+Requires-Dist: scipion-em
+Requires-Dist: scipion-app
+Requires-Dist: scipy<=1.10.0
+Requires-Dist: joblib
+Requires-Dist: peppercorn
+Requires-Dist: plotter
+Requires-Dist: PyWavelets
+
+[![Build](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml/badge.svg)](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml)
+
+# scipion-em-xmipp
+
+Plugin to use Xmipp programs within the Scipion framework.
+
+You can install it either, using the Scipion software following 
+the [Scipion's installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html)
+, (remember to install the scipion-em-xmipp plugin or remove the -noXmipp flag in the Scipion installation)**strongly recommended for non-developers** or cloning it on your own and 
+[linking it to Scipion](https://github.com/I2PC/xmipp#linking-standalone-version-to-scipion).
+The latter is only for those who intended to develop the Xmipp plugin.
+
+For **developers**, we strongly recommend to follow the guide on 
+[how to install xmipp-bundle](https://github.com/i2pc/xmipp#xmipp-as-a-standalone-bundle-for-developers) 
+in order to get a complet Xmipp's development ecosystem.

scipion_em_xmipp-25.6.0/pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scipion-em-xmipp"
+dynamic = ["version", "dependencies"]
+
+authors = [
+    {name = "Oier Lauzirika Zarrabeitia", email = "oierlauzi@bizkaia.eu"},
+    {name = "Alberto Garcia Mena", email = "alberto.garcia@cnb.csic.es"},
+    {name = "Carlos Oscar Sanchez Sorzano", email = "coss@cnb.csic.es"},
+]
+
+description = "Plugin to use Xmipp programs within the Scipion framework."
+readme = "README.md"
+requires-python = ">=3.8"
+keywords = ["scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0"]
+license = {text = "GNU General Public License v3 (GPLv3)"}
+
+[project.urls]
+Homepage = "https://github.com/I2PC/scipion-em-xmipp"
+Issues = "https://github.com/I2PC/scipion-em-xmipp/issues"
+
+[tool.setuptools.dynamic]
+version = {attr = "xmipp3.version.__version__"}
+dependencies = {file = ["requirements.txt"]}
+
+[project.entry-points."pyworkflow.plugin"]
+xmipp3 = "xmipp3"
+
+[tool.setuptools.package-data]
+xmipp3 = ["protocols.conf", "xmipp_logo_devel.png"]

{scipion-em-xmipp-24.6.0.0 → scipion_em_xmipp-25.6.0}/requirements.txt

@@ -1,9 +1,11 @@
 scipion-pyworkflow>=3.0.31
-scikit-learn==0.22
+scikit-learn>=1.2
+scikit-image
 scipion-em
+scipion-app
 scipy<=1.10.0
 joblib
 peppercorn
 plotter
-scons
 PyWavelets
+

scipion_em_xmipp-25.6.0/scipion_em_xmipp.egg-info/PKG-INFO

@@ -0,0 +1,38 @@
+Metadata-Version: 2.1
+Name: scipion-em-xmipp
+Version: 25.6.0
+Summary: Plugin to use Xmipp programs within the Scipion framework.
+Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://github.com/I2PC/scipion-em-xmipp
+Project-URL: Issues, https://github.com/I2PC/scipion-em-xmipp/issues
+Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipion-pyworkflow>=3.0.31
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-image
+Requires-Dist: scipion-em
+Requires-Dist: scipion-app
+Requires-Dist: scipy<=1.10.0
+Requires-Dist: joblib
+Requires-Dist: peppercorn
+Requires-Dist: plotter
+Requires-Dist: PyWavelets
+
+[![Build](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml/badge.svg)](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml)
+
+# scipion-em-xmipp
+
+Plugin to use Xmipp programs within the Scipion framework.
+
+You can install it either, using the Scipion software following 
+the [Scipion's installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html)
+, (remember to install the scipion-em-xmipp plugin or remove the -noXmipp flag in the Scipion installation)**strongly recommended for non-developers** or cloning it on your own and 
+[linking it to Scipion](https://github.com/I2PC/xmipp#linking-standalone-version-to-scipion).
+The latter is only for those who intended to develop the Xmipp plugin.
+
+For **developers**, we strongly recommend to follow the guide on 
+[how to install xmipp-bundle](https://github.com/i2pc/xmipp#xmipp-as-a-standalone-bundle-for-developers) 
+in order to get a complet Xmipp's development ecosystem.

{scipion-em-xmipp-24.6.0.0 → scipion_em_xmipp-25.6.0}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -1,9 +1,9 @@
-CHANGES.md
+CHANGELOG.md
 LICENSE
 MANIFEST.in
 README.md
+pyproject.toml
 requirements.txt
-setup.py
 scipion_em_xmipp.egg-info/PKG-INFO
 scipion_em_xmipp.egg-info/SOURCES.txt
 scipion_em_xmipp.egg-info/dependency_links.txt
@@ -13,23 +13,68 @@ scipion_em_xmipp.egg-info/top_level.txt
 xmipp3/__init__.py
 xmipp3/base.py
 xmipp3/bibtex.py
+xmipp3/checkProtocolsConf.py
 xmipp3/constants.py
 xmipp3/programs.py
 xmipp3/protocols.conf
 xmipp3/utils.py
+xmipp3/version.py
 xmipp3/wizards.py
 xmipp3/xmipp_logo.png
+xmipp3/xmipp_logo_devel.png
 xmipp3/convert/__init__.py
 xmipp3/convert/convert.py
 xmipp3/convert/dataimport.py
 xmipp3/convert/io_coordinates.py
+xmipp3/legacy/protocols/protocol_angular_resolution_alignment.py
+xmipp3/legacy/protocols/protocol_apply_deformation_zernike3d.py
+xmipp3/legacy/protocols/protocol_classification_gpuCorr.py
+xmipp3/legacy/protocols/protocol_classification_gpuCorr_full.py
+xmipp3/legacy/protocols/protocol_classification_gpuCorr_semi.py
+xmipp3/legacy/protocols/protocol_classify_kmeans2d.py
+xmipp3/legacy/protocols/protocol_deep_align.py
+xmipp3/legacy/protocols/protocol_deep_denoising.py
+xmipp3/legacy/protocols/protocol_enrich.py
+xmipp3/legacy/protocols/protocol_kmeans_clustering.py
+xmipp3/legacy/protocols/protocol_metaprotocol_create_output.py
+xmipp3/legacy/protocols/protocol_metaprotocol_create_subset.py
+xmipp3/legacy/protocols/protocol_metaprotocol_discrete_heterogeneity_scheduler.py
+xmipp3/legacy/protocols/protocol_metaprotocol_golden_highres.py
+xmipp3/legacy/protocols/protocol_mltomo.py
+xmipp3/legacy/protocols/protocol_movie_average.py
+xmipp3/legacy/protocols/protocol_movie_opticalflow.py
+xmipp3/legacy/protocols/protocol_particle_boxsize.py
+xmipp3/legacy/protocols/protocol_reconstruct_heterogeneous.py
+xmipp3/legacy/protocols/protocol_rotational_spectra.py
+xmipp3/legacy/protocols/protocol_screen_deeplearning.py
+xmipp3/legacy/protocols/protocol_solid_angles.py
+xmipp3/legacy/protocols/protocol_split_volume.py
+xmipp3/legacy/protocols/protocol_split_volume_hierarchical_cluster.py
+xmipp3/legacy/protocols/protocol_subtract_projection.py
+xmipp3/legacy/tests/test_protocol_deep_denoising.py
+xmipp3/legacy/tests/test_protocols_angular_resolution_alignment.py
+xmipp3/legacy/tests/test_protocols_gpuCorr_classifier.py
+xmipp3/legacy/tests/test_protocols_gpuCorr_fullStreaming.py
+xmipp3/legacy/tests/test_protocols_gpuCorr_semiStreaming.py
+xmipp3/legacy/tests/test_protocols_metaprotocol_golden_highres.py
+xmipp3/legacy/tests/test_protocols_metaprotocol_heterogeneity.py
+xmipp3/legacy/tests/test_protocols_mixed_movies.py
+xmipp3/legacy/tests/test_protocols_solid_angles.py
+xmipp3/legacy/tests/test_protocols_subtract_projection.py
+xmipp3/legacy/tests/test_protocols_xmipp_movies.py
+xmipp3/legacy/viewers/viewer_angular_resolution_alignment.py
+xmipp3/legacy/viewers/viewer_deep_align.py
+xmipp3/legacy/viewers/viewer_metaprotocol_golden_highres.py
+xmipp3/legacy/viewers/viewer_mltomo.py
+xmipp3/legacy/viewers/viewer_solid_angles.py
+xmipp3/legacy/viewers/viewer_split_volume.py
 xmipp3/protocols/__init__.py
 xmipp3/protocols/protocol_align_volume.py
 xmipp3/protocols/protocol_align_volume_and_particles.py
 xmipp3/protocols/protocol_analyze_local_ctf.py
 xmipp3/protocols/protocol_angular_graph_consistency.py
-xmipp3/protocols/protocol_angular_resolution_alignment.py
 xmipp3/protocols/protocol_apply_alignment.py
+xmipp3/protocols/protocol_apply_tilt_to_ctf.py
 xmipp3/protocols/protocol_apply_transformation_matrix.py
 xmipp3/protocols/protocol_apply_zernike3d.py
 xmipp3/protocols/protocol_assignment_tilt_pair.py
@@ -37,11 +82,13 @@ xmipp3/protocols/protocol_break_symmetry.py
 xmipp3/protocols/protocol_center_particles.py
 xmipp3/protocols/protocol_cl2d.py
 xmipp3/protocols/protocol_cl2d_align.py
+xmipp3/protocols/protocol_cl2d_clustering.py
 xmipp3/protocols/protocol_classes_2d_mapping.py
 xmipp3/protocols/protocol_classify_pca.py
 xmipp3/protocols/protocol_classify_pca_streaming.py
 xmipp3/protocols/protocol_compare_angles.py
 xmipp3/protocols/protocol_compare_reprojections.py
+xmipp3/protocols/protocol_compute_likelihood.py
 xmipp3/protocols/protocol_consensus_classes.py
 xmipp3/protocols/protocol_consensus_local_ctf.py
 xmipp3/protocols/protocol_convert_pdb.py
@@ -52,11 +99,11 @@ xmipp3/protocols/protocol_ctf_correct_wiener2d.py
 xmipp3/protocols/protocol_ctf_defocus_group.py
 xmipp3/protocols/protocol_ctf_micrographs.py
 xmipp3/protocols/protocol_deep_center.py
+xmipp3/protocols/protocol_deep_center_predict.py
 xmipp3/protocols/protocol_deep_hand.py
 xmipp3/protocols/protocol_deep_micrograph_screen.py
 xmipp3/protocols/protocol_denoise_particles.py
 xmipp3/protocols/protocol_eliminate_empty_images.py
-xmipp3/protocols/protocol_enrich.py
 xmipp3/protocols/protocol_extract_asymmetric_unit.py
 xmipp3/protocols/protocol_extract_particles.py
 xmipp3/protocols/protocol_extract_particles_movies.py
@@ -66,12 +113,12 @@ xmipp3/protocols/protocol_generate_reprojections.py
 xmipp3/protocols/protocol_helical_parameters.py
 xmipp3/protocols/protocol_kerdensom.py
 xmipp3/protocols/protocol_local_ctf.py
+xmipp3/protocols/protocol_mics_defocus_balancer.py
 xmipp3/protocols/protocol_ml2d.py
 xmipp3/protocols/protocol_movie_alignment_consensus.py
 xmipp3/protocols/protocol_movie_dose_analysis.py
 xmipp3/protocols/protocol_movie_gain.py
 xmipp3/protocols/protocol_movie_max_shift.py
-xmipp3/protocols/protocol_movie_opticalflow.py
 xmipp3/protocols/protocol_movie_split_frames.py
 xmipp3/protocols/protocol_multiple_fscs.py
 xmipp3/protocols/protocol_multireference_alignability.py
@@ -100,7 +147,6 @@ xmipp3/protocols/protocol_resolution_monogenic_signal.py
 xmipp3/protocols/protocol_rotate_volume.py
 xmipp3/protocols/protocol_rotational_symmetry.py
 xmipp3/protocols/protocol_screen_deepConsensus.py
-xmipp3/protocols/protocol_screen_deeplearning.py
 xmipp3/protocols/protocol_screen_particles.py
 xmipp3/protocols/protocol_shift_particles.py
 xmipp3/protocols/protocol_shift_volume.py
@@ -146,24 +192,25 @@ xmipp3/tests/test_protocol_compare_angles.py
 xmipp3/tests/test_protocol_consensus_classes3D.py
 xmipp3/tests/test_protocol_ctf_consensus.py
 xmipp3/tests/test_protocol_extract_asymmetric_unit.py
+xmipp3/tests/test_protocol_likelihood.py
 xmipp3/tests/test_protocol_monodir.py
 xmipp3/tests/test_protocol_multiple_fsc.py
 xmipp3/tests/test_protocol_multireference_alignability.py
 xmipp3/tests/test_protocol_reconstruct_fourier.py
 xmipp3/tests/test_protocol_screen_deepConsensus.py
 xmipp3/tests/test_protocol_simulate_ctf.py
+xmipp3/tests/test_protocol_split_frames.py
 xmipp3/tests/test_protocol_validate_fscq.py
 xmipp3/tests/test_protocol_validate_overfitting.py
 xmipp3/tests/test_protocols_add_noise.py
-xmipp3/tests/test_protocols_angular_resolution_alignment.py
 xmipp3/tests/test_protocols_continuousflex.py
 xmipp3/tests/test_protocols_deepVolPostprocessing.py
+xmipp3/tests/test_protocols_deepcenter_predict.py
 xmipp3/tests/test_protocols_deepres.py
 xmipp3/tests/test_protocols_fso.py
 xmipp3/tests/test_protocols_highres.py
 xmipp3/tests/test_protocols_local_defocus.py
 xmipp3/tests/test_protocols_localdeblur.py
-xmipp3/tests/test_protocols_mixed_movies.py
 xmipp3/tests/test_protocols_monores.py
 xmipp3/tests/test_protocols_realignment_classes.py
 xmipp3/tests/test_protocols_xmipp_2d.py
@@ -175,9 +222,11 @@ xmipp3/tests/test_protocols_zernike3d.py
 xmipp3/viewers/__init__.py
 xmipp3/viewers/plotter.py
 xmipp3/viewers/viewer.py
+xmipp3/viewers/viewer_LL_matrix.py
 xmipp3/viewers/viewer_analyze_local_ctf.py
-xmipp3/viewers/viewer_angular_resolution_alignment.py
+xmipp3/viewers/viewer_apply_tilt_to_ctf.py
 xmipp3/viewers/viewer_cl2d.py
+xmipp3/viewers/viewer_cl2d_clustering.py
 xmipp3/viewers/viewer_consensus_classes.py
 xmipp3/viewers/viewer_ctf_consensus.py
 xmipp3/viewers/viewer_deepEMHancer.py

{scipion-em-xmipp-24.6.0.0 → scipion_em_xmipp-25.6.0}/scipion_em_xmipp.egg-info/entry_points.txt

@@ -1,3 +1,2 @@
 [pyworkflow.plugin]
 xmipp3 = xmipp3
-

{scipion-em-xmipp-24.6.0.0 → scipion_em_xmipp-25.6.0}/scipion_em_xmipp.egg-info/requires.txt

@@ -1,9 +1,10 @@
 scipion-pyworkflow>=3.0.31
-scikit-learn==0.22
+scikit-learn>=1.2
+scikit-image
 scipion-em
+scipion-app
 scipy<=1.10.0
 joblib
 peppercorn
 plotter
-scons
 PyWavelets