scipion-em-xmipp 25.6.1__tar.gz → 26.0.0__tar.gz

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/CHANGELOG.md

@@ -1,5 +1,18 @@
-## Release 3.25.06.1 - Rhea
-- Disabling the default installation of dependencies to prevent breaking the scipion environment
+## Release 4.0.0
+- Protocols updated
+   - deep_micrograph_screen:  updated enviroment to tensorFlow2 and models updated to  
+   - movie_max_shif: Change the criteria to evaluate the shift
+   - crop_resize: Crop/Resize half maps too, if they are available
+   - resolution3D: The FSC can be computed now using the two halves
+   - align_volume_and_particles: Allow considering mirrors in align volume and particles
+
+- More scipion-em-xmipp
+   - Disable xmippDep by default (the dependencies will not be installed by default in the Scipion environment), but installing just the libstdcxx dependence
+   - Script to generate the protocols map (https://i2pc.github.io/docs/protocolsMap.html#)
+   - Remove Relion dependency from TestXmippDenoiseParticles
+   - parse json to report summary installation errors
+   - View all classes added for XmippProtConsensusClasses
+
 
 ## Release 3.25.06.0 - Rhea
 - New protocols

{scipion_em_xmipp-25.6.1/scipion_em_xmipp.egg-info → scipion_em_xmipp-26.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 25.6.1
+Version: 26.0.0
 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)
@@ -20,6 +20,9 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
+Requires-Dist: xmipp3-installer==2.*
+Requires-Dist: numpy==1.*
+Dynamic: license-file
 
 [![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-25.6.1 → scipion_em_xmipp-26.0.0}/requirements.txt

@@ -8,4 +8,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
-
+xmipp3-installer==2.*
+numpy==1.*

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0/scipion_em_xmipp.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 25.6.1
+Version: 26.0.0
 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)
@@ -20,6 +20,9 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
+Requires-Dist: xmipp3-installer==2.*
+Requires-Dist: numpy==1.*
+Dynamic: license-file
 
 [![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-25.6.1 → scipion_em_xmipp-26.0.0}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -15,8 +15,10 @@ xmipp3/base.py
 xmipp3/bibtex.py
 xmipp3/checkProtocolsConf.py
 xmipp3/constants.py
+xmipp3/logParser.py
 xmipp3/programs.py
 xmipp3/protocols.conf
+xmipp3/protocolsCollectInfo.py
 xmipp3/utils.py
 xmipp3/version.py
 xmipp3/wizards.py
@@ -26,6 +28,8 @@ xmipp3/convert/__init__.py
 xmipp3/convert/convert.py
 xmipp3/convert/dataimport.py
 xmipp3/convert/io_coordinates.py
+xmipp3/legacy/__init__.py
+xmipp3/legacy/protocols/__init__.py
 xmipp3/legacy/protocols/protocol_angular_resolution_alignment.py
 xmipp3/legacy/protocols/protocol_apply_deformation_zernike3d.py
 xmipp3/legacy/protocols/protocol_classification_gpuCorr.py
@@ -35,6 +39,7 @@ 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_extract_particles_movies.py
 xmipp3/legacy/protocols/protocol_kmeans_clustering.py
 xmipp3/legacy/protocols/protocol_metaprotocol_create_output.py
 xmipp3/legacy/protocols/protocol_metaprotocol_create_subset.py
@@ -95,6 +100,7 @@ xmipp3/protocols/protocol_convert_pdb.py
 xmipp3/protocols/protocol_core_analysis.py
 xmipp3/protocols/protocol_create_gallery.py
 xmipp3/protocols/protocol_ctf_consensus.py
+xmipp3/protocols/protocol_ctf_correct_phase.py
 xmipp3/protocols/protocol_ctf_correct_wiener2d.py
 xmipp3/protocols/protocol_ctf_defocus_group.py
 xmipp3/protocols/protocol_ctf_micrographs.py
@@ -106,7 +112,6 @@ xmipp3/protocols/protocol_denoise_particles.py
 xmipp3/protocols/protocol_eliminate_empty_images.py
 xmipp3/protocols/protocol_extract_asymmetric_unit.py
 xmipp3/protocols/protocol_extract_particles.py
-xmipp3/protocols/protocol_extract_particles_movies.py
 xmipp3/protocols/protocol_extract_particles_pairs.py
 xmipp3/protocols/protocol_flexalign.py
 xmipp3/protocols/protocol_generate_reprojections.py

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/scipion_em_xmipp.egg-info/requires.txt

@@ -8,3 +8,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
+xmipp3-installer==2.*
+numpy==1.*

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/__init__.py

@@ -45,8 +45,6 @@ NVIDIA_DRIVERS_MINIMUM_VERSION = 450
 
 type_of_version = version.type_of_version
 _logo = version._logo
-_binTagVersion = version._binTagVersion
-_pluginTagVersion= version._pluginTagVersion
 _currentDepVersion = version._currentDepVersion
 __version__ = version.__version__
 
@@ -151,30 +149,33 @@ class Plugin(pwem.Plugin):
         
         # When changing dependencies, increment _currentDepVersion
         CONDA_DEPENDENCIES = [
-	        "'cmake>=3.18,<4'", #cmake-4 is not compatible with Relion compilation
+	    "'cmake>=3.18,<4'", #cmake-4 is not compatible with Relion compilation
             "hdf5>=1.18",
             "sqlite>=3",
             "fftw>=3",
             "make",
             "zlib",
             "openjdk",
-            "libtiff",
-	    "libstdcxx-ng",
+            "'libtiff<=4.5.1'",
             "libjpeg-turbo",
         ]
+
+        CONDA_LIBSTDCXX_PACKAGE = "libstdcxx-ng"
+
         if Config.isCondaInstallation():
             condaEnvPath = os.environ['CONDA_PREFIX']
             scipionEnv=os.path.basename(condaEnvPath)  # TODO: use pyworkflow method when released: Config.getEnvName()
 
             commands = CondaCommandDef(scipionEnv, cls.getCondaActivationCmd())
-            commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
+            #commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
+            commands.condaInstall('-c conda-forge --yes '  + CONDA_LIBSTDCXX_PACKAGE)
             commands.touch("deps_installed.txt")
             env.addPackage(
                 'xmippDep', version=_currentDepVersion,
                 tar='void.tgz',
                 commands=commands.getCommands(),
                 neededProgs=['conda'],
-                default=False
+                default=True
             )
         
         if develMode:
@@ -196,16 +197,15 @@ class Plugin(pwem.Plugin):
 	            default=False
 	        )
         else:
-            xmippSrc = f'xmippSrc-{version._binTagVersion}'
+            xmippSrc = f'xmipp3-{version._binVersion}'
             installCommands = [
                 (f'cd .. && rm -rf {xmippSrc} && '
-                f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
+                f'git clone {XMIPP_GIT_URL} -b {version._binVersion} {xmippSrc} && '
                 f'cd {xmippSrc} && '
-                f'git checkout {version._binTagVersion} && '
                 f'./xmipp --production True ', COMPILE_TARGETS)
             ]
             env.addPackage(
-	                'xmippSrc', version=version._binTagVersion,
+	                'xmipp3', version=version._binVersion,
 	                tar='void.tgz',
 	                commands=installCommands,
 	                neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
@@ -225,7 +225,7 @@ class Plugin(pwem.Plugin):
 
         isBundle = (os.path.isdir(os.path.join(bundleDir, 'src')) and
                     os.path.isfile(os.path.join(bundleDir, 'xmipp')))
-        
+        print(f'pluginDir: {pluginDir}\n, bundleDir: {bundleDir}\n, isBundle: {isBundle}')
         return bundleDir if isBundle else None
 
 def getNvidiaDriverVersion(plugin):

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/constants.py

@@ -28,7 +28,7 @@ This modules contains constants related to Xmipp3 protocols
 """
 
 # ------------------ Constants values --------------------------------------
-XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp.git'
+XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp3.git'
 XMIPP_URL = 'https://github.com/i2pc/scipion-em-xmipp'
 XMIPP_HOME = 'XMIPP_HOME'
 NMA_HOME = 'NMA_HOME'

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/legacy/tests/test_protocols_xmipp_movies.py

@@ -227,3 +227,137 @@ class TestOFAlignment2(TestXmippBase):
                              "been created.")
 
 
+class TestExtractMovieParticles(BaseTest):
+	@classmethod
+	def setData(cls):
+		cls.ds = DataSet.getDataSet('movies')
+
+	@classmethod
+	def runImportMovies(cls, pattern, **kwargs):
+		""" Run an Import micrograph protocol. """
+		# We have two options: passe the SamplingRate or
+		# the ScannedPixelSize + microscope magnification
+		params = {'samplingRate': 1.14,
+		          'voltage': 300,
+		          'sphericalAberration': 2.7,
+		          'magnification': 50000,
+		          'scannedPixelSize': None,
+		          'filesPattern': pattern
+		          }
+		if 'samplingRate' not in kwargs:
+			del params['samplingRate']
+			params['samplingRateMode'] = 0
+		else:
+			params['samplingRateMode'] = 1
+
+		params.update(kwargs)
+
+		protImport = cls.newProtocol(ProtImportMovies, **params)
+		cls.launchProtocol(protImport)
+		return protImport
+
+	@classmethod
+	def setUpClass(cls):
+		setupTestProject(cls)
+		cls.setData()
+		cls.protImport1 = cls.runImportMovies(
+			cls.ds.getFile('qbeta/qbeta.mrc'),
+			magnification=50000)
+		cls.protImport2 = cls.runImportMovies(cls.ds.getFile('cct/cct_1.em'),
+		                                      magnification=61000)
+
+	# def _checkMicrographs(self, protocol, goldDimensions):
+	#     self.assertIsNotNone(getattr(protocol, 'outputMicrographs', None),
+	#                          "Output SetOfMicrographs were not created.")
+	#     mic = protocol.outputMicrographs[1]
+	#     x, y, _ = mic.getDim()
+	#     dims = (x, y)
+	#     msgError = "The dimensions must be %s and it is %s"
+	#     self.assertEqual(goldDimensions, dims,
+	#                      msgError % (goldDimensions, dims))
+	#
+	def _checkAlignment(self, movie, goldRange, goldRoi):
+		alignment = movie.getAlignment()
+		range = alignment.getRange()
+		msgRange = "Alignment range must be %s %s and it is %s (%s)"
+		self.assertEqual(goldRange, range,
+		                 msgRange % (
+			                 goldRange, range, type(goldRange), type(range)))
+		roi = alignment.getRoi()
+		msgRoi = "Alignment ROI must be %s (%s) and it is %s (%s)"
+		self.assertEqual(goldRoi, roi,
+		                 msgRoi % (goldRoi, roi, type(goldRoi), type(roi)))
+
+	def test_qbeta(self):
+		movAliProt = self.newProtocol(XmippProtFlexAlign,
+		                              alignFrame0=2, alignFrameN=6,
+		                              doSaveAveMic=True)
+		movAliProt.inputMovies.set(self.protImport1.outputMovies)
+		self.launchProtocol(movAliProt)
+
+		self._checkAlignment(movAliProt.outputMovies[1],
+		                     (2, 6), [0, 0, 0, 0])
+
+		importPick = self.newProtocol(ProtImportCoordinates,
+		                              importFrom=ProtImportCoordinates.IMPORT_FROM_XMIPP,
+		                              filesPath=self.ds.getFile('qbeta/'),
+		                              filesPattern='*.pos', boxSize=320,
+		                              invertX=False,
+		                              invertY=False
+		                              )
+		importPick.inputMicrographs.set(movAliProt.outputMicrographs)
+		importPick.setObjLabel('import coords from xmipp ')
+		self.launchProtocol(importPick)
+
+		protExtract = self.newProtocol(XmippProtExtractMovieParticles,
+		                               boxSize=320, frame0=2, frameN=6,
+		                               applyAlignment=True, doInvert=True)
+		protExtract.inputMovies.set(movAliProt.outputMovies)
+		protExtract.inputCoordinates.set(importPick.outputCoordinates)
+		protExtract.setObjLabel('extract with alignment')
+		self.launchProtocol(protExtract)
+
+		self.assertIsNotNone(getattr(protExtract, 'outputParticles', None),
+		                     "Output SetOfMovieParticles were not created.")
+
+		size = protExtract.outputParticles.getSize()
+		self.assertEqual(size, 135, 'Number of particles must be 135 and its '
+		                            '%d' % size)
+
+	def test_cct(self):
+		movAliProt = self.newProtocol(XmippProtFlexAlign,
+		                              alignFrame0=2, alignFrameN=6,
+		                              doSaveAveMic=True)
+		movAliProt.inputMovies.set(self.protImport2.outputMovies)
+		self.launchProtocol(movAliProt)
+
+		self._checkAlignment(movAliProt.outputMovies[1],
+		                     (2, 6), [0, 0, 0, 0])
+
+		importPick = self.newProtocol(ProtImportCoordinates,
+		                              importFrom=ProtImportCoordinates.IMPORT_FROM_XMIPP,
+		                              filesPath=self.ds.getFile('cct/'),
+		                              filesPattern='*.pos', boxSize=320,
+		                              invertX=False,
+		                              invertY=False
+		                              )
+		importPick.inputMicrographs.set(movAliProt.outputMicrographs)
+		importPick.setObjLabel('import coords from xmipp ')
+		self.launchProtocol(importPick)
+
+		protExtract = self.newProtocol(XmippProtExtractMovieParticles,
+		                               boxSize=320, frame0=3, frameN=6,
+		                               applyAlignment=False, doInvert=True)
+		protExtract.inputMovies.set(movAliProt.outputMovies)
+		protExtract.inputCoordinates.set(importPick.outputCoordinates)
+		protExtract.setObjLabel('extract without alignment')
+		self.launchProtocol(protExtract)
+
+		self.assertIsNotNone(getattr(protExtract, 'outputParticles', None),
+		                     "Output SetOfMovieParticles were not created.")
+
+		size = protExtract.outputParticles.getSize()
+		self.assertEqual(size, 88, 'Number of particles must be 135 and its '
+		                           '%d' % size)
+
+

scipion_em_xmipp-26.0.0/xmipp3/logParser.py

@@ -0,0 +1,53 @@
+# **************************************************************************
+# *
+# * Authors:     Alberto Garcia Mena (alberto.garcia@cnb.csic.es)
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address 'scipion@cnb.csic.es'
+# *
+# **************************************************************************
+
+'''
+Script to collect all failled attempts from aspecific release of Xmipp and return a json with just the logs reported
+Requires a json generated on https://xmipp.i2pc.es/api/attempts/filters/?user__userId=&xmipp__branch=v3.25.06.0-Rhea&returnCode=&returnCode_not=0 (get-> json save)
+After this scxript, ask any IA:
+ChatGPT Question: This is a JSON file with the logs of the installation failures of Xmipp. Can you make a summary of the most common errors?
+Ommit the Matlab errors and warnings, report the percent of each kind of error
+'''
+
+import json
+import random
+
+jsonpath = '/home/agarcia/Downloads/Rhea.json'
+jsonGenerated = '/home/agarcia/Downloads/RheaJustLogs.json'
+with open(jsonpath, "r") as f:
+    data = json.load(f)
+
+# data is now a list of dicts
+print(f"Number of entries: {len(data)}")
+
+logs = [entry["logTail"] for entry in data if "logTail" in entry]
+
+# pick a random subset of 100 entries
+subset = random.sample(logs, min(400, len(logs)))
+
+# write to new JSON file
+with open(jsonGenerated, "w") as f:
+    json.dump(subset, f, indent=4, ensure_ascii=False)

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/protocols/__init__.py

@@ -52,13 +52,13 @@ from .protocol_create_gallery import XmippProtCreateGallery
 from .protocol_ctf_consensus import XmippProtCTFConsensus
 from .protocol_ctf_micrographs import XmippProtCTFMicrographs
 from .protocol_ctf_correct_wiener2d import XmippProtCTFCorrectWiener2D
+from .protocol_ctf_correct_phase import XmippProtCTFCorrectPhase2D
 from .protocol_consensus_classes import XmippProtConsensusClasses
 from .protocol_denoise_particles import XmippProtDenoiseParticles
 from .protocol_deep_micrograph_screen import XmippProtDeepMicrographScreen
 from .protocol_eliminate_empty_images import (XmippProtEliminateEmptyParticles,
                                               XmippProtEliminateEmptyClasses)
 from .protocol_extract_particles import XmippProtExtractParticles
-from .protocol_extract_particles_movies import XmippProtExtractMovieParticles
 from .protocol_extract_particles_pairs import XmippProtExtractParticlesPairs
 from .protocol_extract_asymmetric_unit import XmippProtExtractUnit
 from .protocol_helical_parameters import XmippProtHelicalParameters

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/protocols/protocol_align_volume.py

@@ -51,7 +51,7 @@ class XmippProtAlignVolume(ProtAlignVolume):
      """
     _label = 'align volume'
     nVols = 0
-    _devStatus = UPDATED
+    _devStatus = PROD
     OUTPUT_NAME1 = "outputVolume"
     OUTPUT_NAME2 = "outputVolumes"
     _possibleOutputs = {OUTPUT_NAME1: Volume,

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/protocols/protocol_align_volume_and_particles.py

@@ -38,6 +38,7 @@ from pyworkflow.utils import weakImport
 from pyworkflow.utils.path import cleanPath
 
 from xmipp3.constants import SYM_URL
+from pyworkflow import BETA, UPDATED, NEW, PROD
 
 ALIGN_MASK_CIRCULAR = 0
 ALIGN_MASK_BINARY_FILE = 1
@@ -63,13 +64,14 @@ class XmippProtAlignVolumeParticles(ProtAlignVolume):
      """
     _label = 'align volume and particles'
     _possibleOutputs = AlignVolPartOutputs
+    _devStatus = UPDATED
     nVols = 0
+
     
     def __init__(self, **args):
         ProtAlignVolume.__init__(self, **args)
 
         # These 2 must match the output enum above.
-        self._alignmentMatrix = None
         self.Volume = None
         self.Particles = None
 
@@ -89,6 +91,8 @@ class XmippProtAlignVolumeParticles(ProtAlignVolume):
                            'calculated with the reference and input volumes.')
         form.addParam('alignmentMode', params.EnumParam, default=ALIGN_GLOBAL, choices=["Global","Local"],
                       label="Alignment mode")
+        form.addParam('considerMirrors', params.BooleanParam, default=False,
+                      label='Consider mirrors')
         form.addParam('symmetryGroup', params.StringParam, default='c1',
                       label="Symmetry group",
                       help='See %s page for a description of the symmetries '
@@ -160,6 +164,8 @@ class XmippProtAlignVolumeParticles(ProtAlignVolume):
             args += " --frm"
         else:
             args += " --local"
+        if self.considerMirrors:
+            args += " --consider_mirror"
         args += " --copyGeo %s" % fhInputTranMat
         if not self.wrap:
             args += ' --dontWrap'
@@ -168,13 +174,16 @@ class XmippProtAlignVolumeParticles(ProtAlignVolume):
         cleanPath(self.fnInputVol)
 
     def getAlignmentMatrix(self):
-
-        if self._alignmentMatrix is None:
+        if not (hasattr(self, '_lhsAlignmentMatrix') and hasattr(self, '_rhsAlignmentMatrix')):
             fhInputTranMat = self.getTransformationFile()
             transMatFromFile = np.loadtxt(fhInputTranMat)
-            self._alignmentMatrix = np.reshape(transMatFromFile, (4, 4))
+            self._lhsAlignmentMatrix = np.reshape(transMatFromFile, (4, 4))
+            self._rhsAlignmentMatrix = np.eye(4)
+            
+            if np.linalg.det(self._lhsAlignmentMatrix[:3,:3]) < 0:
+                self._rhsAlignmentMatrix[2,2] = -1
 
-        return self._alignmentMatrix
+        return self._lhsAlignmentMatrix, self._rhsAlignmentMatrix
 
     def getTransformationFile(self):
         return self._getExtraPath('transformation-matrix.txt')
@@ -217,12 +226,11 @@ class XmippProtAlignVolumeParticles(ProtAlignVolume):
         self._defineSourceRelation(self.inputParticles, outputParticles)
 
     def _updateParticleTransform(self, particle, row):
+        lhs, rhs = self.getAlignmentMatrix()
+        alignment = np.array(particle.getTransform().getMatrix())
+        alignment2 = lhs @ alignment @ rhs
 
-        aliMatrix = self.getAlignmentMatrix()
-        partTransformMat = particle.getTransform().getMatrix()
-        partTransformMatrix = np.matrix(partTransformMat)
-        newTransformMatrix = np.matmul(aliMatrix, partTransformMatrix)
-        particle.getTransform().setMatrix(newTransformMatrix)
+        particle.getTransform().setMatrix(alignment2)
 
     def getOutputAlignedVolumePath(self):
         outVolFn = self._getExtraPath("inputVolumeAligned.mrc")

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/protocols/protocol_break_symmetry.py

@@ -40,7 +40,7 @@ class XmippProtAngBreakSymmetry(ProtProcessParticles):
     equivalent angular assignment for a given symmetry.
 
     Be aware that input symmetry values follows Xmipp conventions as described in:
-    http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry
+    https://i2pc.github.io/docs/Utils/Conventions/index.html#symmetry
     """
     _label = 'break symmetry'
 
@@ -49,7 +49,7 @@ class XmippProtAngBreakSymmetry(ProtProcessParticles):
         
         form.addParam('symmetryGroup', StringParam, default="c1",
                       label='Symmetry group',
-                      help="See http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry"
+                      help="See https://i2pc.github.io/docs/Utils/Conventions/index.html#symmetry"
                            " for a description of the symmetry groups format in Xmipp.\n"
                            "If no symmetry is present, use _c1_.")
     
@@ -63,9 +63,9 @@ class XmippProtAngBreakSymmetry(ProtProcessParticles):
         # Create a metadata with the geometrical information
         # as expected by Xmipp
         imgsFn = self._getPath('input_particles.xmd')
-        self._insertFunctionStep('convertInputStep', imgsFn)
-        self._insertFunctionStep('breakSymmetryStep', imgsFn)
-        self._insertFunctionStep('createOutputStep')
+        self._insertFunctionStep(self.convertInputStep, imgsFn)
+        self._insertFunctionStep(self.breakSymmetryStep, imgsFn)
+        self._insertFunctionStep(self.createOutputStep)
 
     #--------------------------- STEPS functions --------------------------------------------
 

{scipion_em_xmipp-25.6.1 → scipion_em_xmipp-26.0.0}/xmipp3/protocols/protocol_classify_pca.py

@@ -84,23 +84,14 @@ ALIGNMENT_DICT = {"shiftX": XMIPPCOLUMNS.shiftX.value,
                   "angleTilt": XMIPPCOLUMNS.angleTilt.value
                   }
 
-
-
-def updateEnviron(gpuNum):
-    """ Create the needed environment for pytorch programs. """
-    print("updating environ to select gpu %s" % (gpuNum))
-    if gpuNum == '':
-        os.environ['CUDA_VISIBLE_DEVICES'] = '0'
-    else:
-        os.environ['CUDA_VISIBLE_DEVICES'] = str(gpuNum)
-
 CONTRAST_AVERAGES_FILE = 'classes_contrast_classes.star'
 AVERAGES_IMAGES_FILE = 'classes_images.star'
         
 class XmippProtClassifyPca(ProtClassify2D, XmippProtocol):
-    """ Classifies a set of images. """
+    """ Classifies a set of images using Principal Component Analysis (PCA). This 2D classification groups (the number of groups can be set) are based on their similarities, assisting in the identification of different conformational states or particle populations. """
     
-    _label = 'Classifies a set of images using Principal Component Analysis (PCA). This 2D classification groups (the number of groups can be set) are based on their similarities, assisting in the identification of different conformational states or particle populations.'
+    _label= '2D classification pca'
+
     _lastUpdateVersion = VERSION_3_0
     _conda_env = 'xmipp_pyTorch'
     _devStatus = BETA
@@ -171,7 +162,6 @@ class XmippProtClassifyPca(ProtClassify2D, XmippProtocol):
     def _insertAllSteps(self):
 
         """ Mainly prepare the command line for call classification program"""
-        self.setGPU()
         self.imgsOrigXmd = self._getExtraPath('images_original.xmd')
         self.imgsXmd = self._getTmpPath('images.xmd')
         self.imgsFn = self._getTmpPath('images.mrc')
@@ -198,13 +188,21 @@ class XmippProtClassifyPca(ProtClassify2D, XmippProtocol):
     
         self._insertFunctionStep('createOutputStep')
 
-    def setGPU(self):
-        if self.useQueueForSteps() or self.useQueue():
-            myStr = os.environ["CUDA_VISIBLE_DEVICES"]
+
+    def getGpusList(self, separator):
+        strGpus = ""
+        for elem in self._stepsExecutor.getGpuList():
+            strGpus = strGpus + str(elem) + separator
+        return strGpus[:-1]
+
+    def setGPU(self, oneGPU=False):
+        if oneGPU:
+            gpus = self.getGpusList(",")[0]
         else:
-            myStr = self.gpuList.get()
-            os.environ["CUDA_VISIBLE_DEVICES"] = self.gpuList.get()
-        self.numGPU = myStr.split(',')[0]
+            gpus = self.getGpusList(",")
+        os.environ["CUDA_VISIBLE_DEVICES"] = gpus
+        self.info(f'Visible GPUS: {gpus}')
+        return gpus
 
 
     #--------------------------- STEPS functions -------------------------------
@@ -234,8 +232,9 @@ class XmippProtClassifyPca(ProtClassify2D, XmippProtocol):
         
         
     def pcaTraining(self, inputIm, resolutionTrain, numTrain):
+        gpuId = self.setGPU(oneGPU=True)
         args = ' -i %s  -s %s -hr %s -lr 530 -p %s -t %s -o %s/train_pca  --batchPCA -g %s'% \
-                (inputIm, self.sampling, resolutionTrain, self.coef.get(), numTrain, self._getExtraPath(), self.numGPU)
+                (inputIm, self.sampling, resolutionTrain, self.coef.get(), numTrain, self._getExtraPath(), gpuId)
 
         env = self.getCondaEnv()
         env['LD_LIBRARY_PATH'] = ''
@@ -243,9 +242,10 @@ class XmippProtClassifyPca(ProtClassify2D, XmippProtocol):
         
         
     def classification(self, inputIm, numClass, stfile, mask, sigma):
+        gpuId = self.setGPU(oneGPU=True)
         args = ' -i %s -c %s -b %s/train_pca_bands.pt -v %s/train_pca_vecs.pt -o %s/classes -stExp %s -g %s' % \
                 (inputIm, numClass, self._getExtraPath(), self._getExtraPath(),  self._getExtraPath(),
-                 stfile, self.numGPU)
+                 stfile, gpuId)
         if mask:
             args += ' --mask --sigma %s '%(sigma)