scipion-em-xmipp 23.11.0.0__tar.gz → 24.6.0.0__tar.gz

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/CHANGES.md

@@ -1,3 +1,41 @@
+## Release 3.24.06 - Oceanus
+   - New protocols
+      - movie_alignment_consensus: protocol for the comparison of two global alignments
+      - PCA classification: 2D Classification method that can works in streaming and in static
+
+   - Protocols updated
+      - deep_center: Deep center calculates an approximate center for the particles.
+      - validate_fscq: Added cif support
+      - reconstruct_fourier: Enable reconstructing with halves in the reconstruct fourier
+      - simulate_ctf: Simulate CTF can add noise before and after CTF.
+      - extract_particles: Local average added
+      - compare_reprojections: Downsampling option,autodown sampling, allows input 2D in several formats, allows input 3D in several formats, ranking option available, extraction option available
+      - cl2d: ensuring a save classes creating and adding possible output
+   - Protocols fixed
+      - resolution_deepres:now works with queue system
+      - ProcessVolumes: Fix header for resize voxels
+      - resolution_bfactor:Fix local resolution to local bfactor  
+      - resolution_bfactor: create output for res bfac
+      - extract_particles: Bug fix in the downsampling factor of extract particles
+      - core_analysis: define correctly the particles pointer to have indirect pointer
+      - tilt_analysis: estimate automatically the window size new option
+      - movie_doseanalysis: update correctly the outputSet
+      - extract_particles: Check if resizing is enabled
+      - particle_pick_remove_duplicates: Remove duplicates coordinates 
+   - Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols))
+      - deep_denoissing
+      - metaprotocol_create_subset
+      - metaprotocol_golden_highres
+      - solid_angle
+      - split_volume
+   - More scipio-em-xmipp
+      - Solve Sonar Cloud reported bugs
+      - Flexible import of pyQT on chimera script
+      - Removing tkAgg matplotlib requirement in viewer_structure_map
+      - DLTK installation bug local variable and Fix use gpu
+      - updated scikit-learn version
+
+
 ## Release 3.23.11 - Nereus
    - New protocols
       - Volume local adjustment

{scipion-em-xmipp-23.11.0.0/scipion_em_xmipp.egg-info → scipion-em-xmipp-24.6.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: scipion-em-xmipp
-Version: 23.11.0.0
+Version: 24.6.0.0
 Summary: Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).
 Home-page: https://github.com/i2pc/scipion-em-xmipp
 Author: I2PC

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0/scipion_em_xmipp.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: scipion-em-xmipp
-Version: 23.11.0.0
+Version: 24.6.0.0
 Summary: Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).
 Home-page: https://github.com/i2pc/scipion-em-xmipp
 Author: I2PC

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -38,6 +38,8 @@ xmipp3/protocols/protocol_center_particles.py
 xmipp3/protocols/protocol_cl2d.py
 xmipp3/protocols/protocol_cl2d_align.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_consensus_classes.py
@@ -49,8 +51,7 @@ xmipp3/protocols/protocol_ctf_consensus.py
 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_assignment.py
-xmipp3/protocols/protocol_deep_denoising.py
+xmipp3/protocols/protocol_deep_center.py
 xmipp3/protocols/protocol_deep_hand.py
 xmipp3/protocols/protocol_deep_micrograph_screen.py
 xmipp3/protocols/protocol_denoise_particles.py
@@ -65,9 +66,8 @@ 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_metaprotocol_create_subset.py
-xmipp3/protocols/protocol_metaprotocol_golden_highres.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
@@ -105,8 +105,6 @@ xmipp3/protocols/protocol_screen_particles.py
 xmipp3/protocols/protocol_shift_particles.py
 xmipp3/protocols/protocol_shift_volume.py
 xmipp3/protocols/protocol_simulate_ctf.py
-xmipp3/protocols/protocol_solid_angles.py
-xmipp3/protocols/protocol_split_volume.py
 xmipp3/protocols/protocol_structure_map.py
 xmipp3/protocols/protocol_structure_map_zernike3d.py
 xmipp3/protocols/protocol_subtract_projection.py
@@ -147,8 +145,6 @@ xmipp3/tests/test_protocol_apply_transformation_matrix.py
 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_deep_center_assignment.py
-xmipp3/tests/test_protocol_deep_denoising.py
 xmipp3/tests/test_protocol_extract_asymmetric_unit.py
 xmipp3/tests/test_protocol_monodir.py
 xmipp3/tests/test_protocol_multiple_fsc.py
@@ -167,11 +163,9 @@ 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_metaprotocol_golden_highres.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_solid_angles.py
 xmipp3/tests/test_protocols_xmipp_2d.py
 xmipp3/tests/test_protocols_xmipp_3d.py
 xmipp3/tests/test_protocols_xmipp_mics.py
@@ -193,7 +187,6 @@ xmipp3/viewers/viewer_dose_analysis.py
 xmipp3/viewers/viewer_eliminate_empty_images.py
 xmipp3/viewers/viewer_extract_asymmetric_unit.py
 xmipp3/viewers/viewer_local_sharpening.py
-xmipp3/viewers/viewer_metaprotocol_golden_highres.py
 xmipp3/viewers/viewer_ml2d.py
 xmipp3/viewers/viewer_movie_alignment.py
 xmipp3/viewers/viewer_normalize_strain.py
@@ -207,8 +200,6 @@ xmipp3/viewers/viewer_resolution_deepres.py
 xmipp3/viewers/viewer_resolution_directional.py
 xmipp3/viewers/viewer_resolution_fso.py
 xmipp3/viewers/viewer_resolution_monogenic_signal.py
-xmipp3/viewers/viewer_solid_angles.py
-xmipp3/viewers/viewer_split_volume.py
 xmipp3/viewers/viewer_structure_map.py
 xmipp3/viewers/viewer_subtract_projection.py
 xmipp3/viewers/viewer_swarm.py

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/xmipp3/__init__.py

@@ -41,7 +41,7 @@ type_of_version = 'release' #'devel'
 _logo = "xmipp_logo" + ("" if type_of_version == 'release' else '_devel') + '.png'
 
 _references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
-_currentBinVersion = '3.23.11.0'
+_currentBinVersion = '3.24.06.0'
 __version__ = _currentBinVersion[2:] + ".0"  # Set this to ".0" on each xmipp binary release, otherwise increase it --> ".1", ".2", ...
 
 # Requirement version variables
@@ -204,6 +204,7 @@ def installDeepLearningToolkit(plugin, env):
     preMsgs = []
     cudaMsgs = []
     nvidiaDriverVer = None
+    useGpu = False
     if os.environ.get('CUDA', 'True') == 'True':
         try:
             nvidiaDriverVer = subprocess.Popen(["nvidia-smi",
@@ -229,7 +230,6 @@ def installDeepLearningToolkit(plugin, env):
             msg = ("Tensorflow installed without GPU. Just CPU computations "
                    "enabled (slow computations).")
             cudaMsgs.append(msg)
-            useGpu = False
 
     if nvidiaDriverVer is not None:
         preMsgs.append("CUDA support found. Driver version: %s" % nvidiaDriverVer)

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/xmipp3/convert/convert.py

@@ -830,30 +830,35 @@ def writeSetOfCoordinatesWithState(posDir, coordSet, state, scale=1):
 
     f = None
     lastMicId = None
-    c = 0
-
-    for coord in coordSet.iterItems(orderBy='_micId'):
-        micId = coord.getMicId()
-
-        if micId != lastMicId:
-            # we need to close previous opened file
-            if f:
-                f.close()
-                c = 0
-            f = openMd(posDict[micId], state)
-            lastMicId = micId
-        c += 1
-        if scale != 1:
-            x = coord.getX() * scale
-            y = coord.getY() * scale
-        else:
-            x = coord.getX()
-            y = coord.getY()
-        f.write(" %06d   1   %d  %d  %d   %06d\n"
-                % (coord.getObjId(), x, y, 1, micId))
 
-    if f:
-        f.close()
+    try:
+        for coord in coordSet.iterItems(orderBy='_micId'):
+            micId = coord.getMicId()
+
+            if micId != lastMicId:
+                # we need to close previous opened file
+                if f:
+                    f.close()
+                f = openMd(posDict[micId], state)
+                lastMicId = micId
+
+            if scale != 1:
+                x = coord.getX() * scale
+                y = coord.getY() * scale
+            else:
+                x = coord.getX()
+                y = coord.getY()
+
+            f.write(" %06d   1   %d  %d  %d   %06d\n"
+                    % (coord.getObjId(), x, y, 1, micId))
+
+    except (FileNotFoundError, PermissionError) as error:
+        print(f"Error occurred: {error}")
+    except Exception as e:
+        print(f"Unexpected error occurred: {e}")
+    finally:
+        if f:
+            f.close()
 
     # Write config.xmd metadata
     configFn = join(posDir, 'config.xmd')
@@ -1386,7 +1391,7 @@ def rowToAlignment(alignmentRow, alignType):
         else:
             psi = alignmentRow.getValue(emlib.MDL_ANGLE_PSI, 0.)
             rot = alignmentRow.getValue(emlib.MDL_ANGLE_ROT, 0.)
-            if rot != 0. and psi != 0:
+            if not np.isclose(rot, 0., atol=1e-6 ) and not np.isclose(psi, 0., atol=1e-6):
                 print("HORROR rot and psi are different from zero in 2D case")
             angles[0] = \
                 alignmentRow.getValue(emlib.MDL_ANGLE_PSI, 0.)\

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/xmipp3/protocols/__init__.py

@@ -39,6 +39,8 @@ from .protocol_apply_transformation_matrix import XmippProtApplyTransformationMa
 from .protocol_break_symmetry import XmippProtAngBreakSymmetry
 from .protocol_cl2d_align import XmippProtCL2DAlign
 from .protocol_cl2d import XmippProtCL2D
+from .protocol_classify_pca import XmippProtClassifyPca
+from .protocol_classify_pca_streaming import XmippProtClassifyPcaStreaming
 #from .protocol_classify_kmeans2d import XmippProtKmeansClassif2D
 from .protocol_ctf_defocus_group import XmippProtCTFDefocusGroup
 from .protocol_compare_reprojections import XmippProtCompareReprojections
@@ -51,7 +53,7 @@ from .protocol_ctf_micrographs import XmippProtCTFMicrographs
 from .protocol_ctf_correct_wiener2d import XmippProtCTFCorrectWiener2D
 from .protocol_consensus_classes import XmippProtConsensusClasses
 from .protocol_denoise_particles import XmippProtDenoiseParticles
-from .protocol_deep_micrograph_screen import  XmippProtDeepMicrographScreen
+from .protocol_deep_micrograph_screen import XmippProtDeepMicrographScreen
 from .protocol_eliminate_empty_images import (XmippProtEliminateEmptyParticles,
                                               XmippProtEliminateEmptyClasses)
 from .protocol_enrich import XmippProtEnrich
@@ -63,6 +65,7 @@ from .protocol_helical_parameters import XmippProtHelicalParameters
 from .protocol_kerdensom import XmippProtKerdensom
 from .protocol_ml2d import XmippProtML2D
 from .protocol_movie_gain import XmippProtMovieGain
+from .protocol_movie_alignment_consensus import XmippProtConsensusMovieAlignment
 from .protocol_flexalign import XmippProtFlexAlign
 from .protocol_movie_opticalflow import XmippProtOFAlignment, ProtMovieAlignment
 from .protocol_movie_max_shift import XmippProtMovieMaxShift
@@ -103,8 +106,6 @@ from .protocol_screen_deeplearning import XmippProtScreenDeepLearning
 from .protocol_shift_particles import XmippProtShiftParticles
 from .protocol_shift_volume import XmippProtShiftVolume
 from .protocol_simulate_ctf import XmippProtSimulateCTF
-from .protocol_solid_angles import XmippProtSolidAngles
-from .protocol_split_volume import XmippProtSplitvolume
 from .protocol_subtract_projection import XmippProtSubtractProjection
 from .protocol_subtract_projection import XmippProtBoostParticles
 from .protocol_tilt_analysis import XmippProtTiltAnalysis
@@ -117,8 +118,6 @@ from .protocol_volume_strain import XmippProtVolumeStrain
 from .protocol_write_testC import XmippProtWriteTestC
 from .protocol_write_testP import XmippProtWriteTestP
 from .protocol_generate_reprojections import XmippProtGenerateReprojections
-from .protocol_deep_denoising import XmippProtDeepDenoising  # deepDenoising has to be after XmippProtGenerateReprojections and XmippProtCompareReprojections
-from .protocol_metaprotocol_create_subset import XmippMetaProtCreateSubset
 from .protocol_volume_deform_zernike3d import XmippProtVolumeDeformZernike3D
 from .protocol_structure_map_zernike3d import XmippProtStructureMapZernike3D
 from .protocol_align_volume_and_particles import XmippProtAlignVolumeParticles
@@ -126,7 +125,6 @@ from .protocol_local_ctf import XmippProtLocalCTF
 from .protocol_analyze_local_ctf import XmippProtAnalyzeLocalCTF
 from .protocol_consensus_local_ctf import XmippProtConsensusLocalCTF
 from .protocol_particle_pick_remove_duplicates import XmippProtPickingRemoveDuplicates
-from .protocol_metaprotocol_golden_highres import XmippMetaProtGoldenHighRes
 # from .protocol_apply_deformation_zernike3d import XmippProtApplyZernike3D
 # from .protocol_kmeans_clustering import XmippProtKmeansSPH
 from .protocol_structure_map import XmippProtStructureMap
@@ -136,4 +134,4 @@ from .protocol_volume_consensus import XmippProtVolConsensus
 from .protocol_volume_local_adjust import XmippProtLocalVolAdj
 from .protocol_classes_2d_mapping import XmippProtCL2DMap
 from .protocol_deep_hand import XmippProtDeepHand
-from .protocol_deep_center_assignment import XmippProtDeepCenter, XmippProtDeepGlobalAssignment
+from .protocol_deep_center import XmippProtDeepCenter

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/xmipp3/protocols/protocol_angular_graph_consistency.py

@@ -521,7 +521,7 @@ class XmippProtAngularGraphConsistency(ProtAnalysis3D):
         if (not hasattr(self, 'outputParticles')):
             summary.append("Output not ready yet.")
         else:
-            if self.percentage == 100.0:
+            if self.percentage == 100:
                 text = 'After validation, all of the images are likely to be within the realiable assignment zone'
             else:
                 text = 'After validation, a %.2f' % self.percentage

{scipion-em-xmipp-23.11.0.0 → scipion-em-xmipp-24.6.0.0}/xmipp3/protocols/protocol_cl2d.py

@@ -36,6 +36,7 @@ import pwem.emlib.metadata as md
 from pwem.protocols import ProtClassify2D
 from pwem.objects import SetOfClasses2D
 from pwem.constants import ALIGN_NONE, ALIGN_2D
+from pyworkflow import BETA, UPDATED, NEW, PROD
 
 
 from xmipp3.convert import (writeSetOfParticles, createItemMatrix,
@@ -52,6 +53,7 @@ CL_CLASSICAL = 0
 CL_ROBUST = 1
 
 # Classes keys
+OUTPUTCLASSES = 'outputClasses'
 CLASSES = ''
 CLASSES_CORE = '_core'
 CLASSES_STABLE_CORE = '_stable_core'
@@ -65,6 +67,11 @@ class XmippProtCL2D(ProtClassify2D):
     the original dataset into a given number of classes. """
     
     _label = 'cl2d'
+    _devStatus = UPDATED
+
+    _possibleOutputs = {OUTPUTCLASSES: SetOfClasses2D,
+                        OUTPUTCLASSES+CLASSES_CORE: SetOfClasses2D,
+                        OUTPUTCLASSES+CLASSES_STABLE_CORE: SetOfClasses2D}
     
     def __init__(self, **args):
         ProtClassify2D.__init__(self, **args)
@@ -195,7 +202,7 @@ class XmippProtCL2D(ProtClassify2D):
         else:
             initialClassesId = None
         
-        self._insertFunctionStep('convertInputStep',
+        self._insertFunctionStep(self.convertInputStep,
                                  self.inputParticles.get().getObjId(),
                                  initialClassesId)
 
@@ -229,7 +236,7 @@ class XmippProtCL2D(ProtClassify2D):
             args = self._defArgsCoreAnalisys()
             self._insertClassifySteps(program, args, subset=CLASSES_CORE)
             if self.analyzeRejected:
-                self._insertFunctionStep('analyzeOutOfCores', CLASSES_CORE)
+                self._insertFunctionStep(self.analyzeOutOfCores, CLASSES_CORE)
 
             if (self.numberOfClasses > (2 * self.numberOfInitialClasses.get())
                 and self.doStableCore): # Number of levels should be > 2
@@ -239,7 +246,7 @@ class XmippProtCL2D(ProtClassify2D):
                 self._insertClassifySteps(program, args,
                                           subset=CLASSES_STABLE_CORE)
                 if self.analyzeRejected:
-                    self._insertFunctionStep('analyzeOutOfCores',
+                    self._insertFunctionStep(self.analyzeOutOfCores,
                                              CLASSES_STABLE_CORE)
 
     def _insertClassifySteps(self, program, args, subset=CLASSES):
@@ -250,9 +257,9 @@ class XmippProtCL2D(ProtClassify2D):
         4. And create output
         """
         self._insertRunJobStep(program, args % self._params)
-        self._insertFunctionStep('evaluateClassesStep', subset)
-        self._insertFunctionStep('sortClassesStep', subset)
-        self._insertFunctionStep('createOutputStep', subset)
+        self._insertFunctionStep(self.evaluateClassesStep, subset)
+        self._insertFunctionStep(self.sortClassesStep, subset)
+        self._insertFunctionStep(self.createOutputStep, subset)
     
     #--------------------------- STEPS functions -------------------------------
     def convertInputStep(self, particlesId, classesId):
@@ -309,16 +316,15 @@ class XmippProtCL2D(ProtClassify2D):
         resulting from the protocol execution.
         """
        
-        inputParticles = self.inputParticles.get()
         level = self._lastLevel()
         
         subsetFn = self._getFileName("level_classes", level=level, sub=subset)
         
         if exists(subsetFn):
-            classes2DSet = self._createSetOfClasses2D(inputParticles, subset)
+            classes2DSet = self._createSetOfClasses2D(self.inputParticles, subset)
             self._fillClassesFromLevel(classes2DSet, "last", subset)
     
-            result = {'outputClasses' + subset: classes2DSet}
+            result = {OUTPUTCLASSES + subset: classes2DSet}
             self._defineOutputs(**result)
             self._defineSourceRelation(self.inputParticles, classes2DSet)