Merge branch 'devel' into fix_test_score_coordinates

xmipptomo/protocols/protocol_cltomo.py

@@ -30,41 +30,46 @@
 from pyworkflow.protocol import (IntParam, PointerParam, LEVEL_ADVANCED, BooleanParam, StringParam, FloatParam)
 from pyworkflow.utils import Environ
 from xmipp3 import Plugin
+from pwem.protocols import EMProtocol
+from tomo.protocols import ProtTomoBase
+from tomo.objects import SetOfSubTomograms, SetOfClassesSubTomograms
 from xmipp3.convert import readSetOfVolumes, readSetOfClassesVol, writeSetOfVolumes
 
+OUTPUTATTRIBUTE ='SetOfClassesSubTomograms'
 
-class XmippProtCLTomo(ProtClassify3D):
+class XmippProtCLTomo(EMProtocol, ProtTomoBase):
     """ Averages a set of subtomograms taking into account the missing edge. """
 
     _label = 'cltomo'
     _devStatus = BETA
+    _possibleOutputs = {OUTPUTATTRIBUTE: SetOfClassesSubTomograms}
 
     # --------------------------- DEFINE param functions --------------------------------------------
     def _defineParams(self, form):
         form.addSection(label='General parameters')
-        form.addParam('inputVolumes', PointerParam, pointerClass="SetOfVolumes", label='Set of volumes',
-                      help="Set of volumes to align")
+        form.addParam('inputVolumes', PointerParam, pointerClass=SetOfSubTomograms, label='Subtomograms',
+                      help="Set of subtomograms to align")
         form.addParam('numberOfReferences', IntParam, label='Number of references', default=3,
                       help="How many references are computed at the end of the process")
         form.addParam('numberOfIterations', IntParam, label='Number of iterations', default=15,
                       expertLevel=LEVEL_ADVANCED, help="How many iterations at each of the Clustering levels")
-        form.addParam('generateAligned', BooleanParam, default=True, label='Generate aligned subvolumes',
+        form.addParam('generateAligned', BooleanParam, default=True, label='Generate aligned subtomograms',
                       help="If set to true, it will be created a new set of volumes with all of them aligned")
         form.addParam('align', BooleanParam, default=True, label="Align",
-                      help="Do not align if volumes are already aligned, only classify")
+                      help="Do not align if subtomograms are already aligned, only classify")
 
         form.addSection(label='Initial references')
         form.addParam('doGenerateInitial', BooleanParam, default=True, label='Generate initial volume',
                       help="Let CLTomo to automatically generate the initial references")
         form.addParam('numberOfReferences0', IntParam, label='Number of initial references', default=1,
                       condition="doGenerateInitial",
-                      help="How many initial volumes. If set to 1, all subvolumes are aligned to a single reference, " \
+                      help="How many initial subtomograms. If set to 1, all subtomograms are aligned to a single reference, " \
                            "and then they are classified")
         form.addParam('randomizeOrientation', BooleanParam, default=False, label='Randomize orientation',
                       condition="doGenerateInitial",
-                      help="Use this option if all the input volumes have the same missing wedge or if they have not been previously aligned.")
-        form.addParam('referenceList', PointerParam, pointerClass="SetOfVolumes", label='Set of initial volumes',
-                      condition="not doGenerateInitial", help="Set of initial volumes")
+                      help="Use this option if all the input subtomograms have the same missing wedge or if they have not been previously aligned.")
+        form.addParam('referenceList', PointerParam, pointerClass="SetOfVolumes", label='Set of initial subtomograms',
+                      condition="not doGenerateInitial", help="Set of initial subtomograms")
 
         form.addSection(label='Constraints')
         form.addParam('symmetry', StringParam, default='c1', label='Symmetry group',
@@ -134,7 +139,7 @@ def createOutput(self):
         if levelFiles:
             levelFiles.sort()
             lastLevelFile = levelFiles[-1]
-            setOfClasses = self._createSetOfClassesVol()
+            setOfClasses = self._createSetOfClassesSubTomograms(self.inputVolumes.get())
             setOfClasses.setImages(self.inputVolumes.get())
             readSetOfClassesVol(setOfClasses, lastLevelFile)
             self._defineOutputs(outputClasses=setOfClasses)
@@ -154,27 +159,27 @@ def _summary(self):
         if self.doGenerateInitial.get():
             messages.append('Number of initial references: %d' % self.numberOfReferences0.get())
             if self.randomizeOrientation.get():
-                messages.append('Input subvolume orientations were randomized')
+                messages.append('Input subtomograms orientations were randomized')
         if not self.align:
-            messages.append('Input subvolumes were assumed to be already aligned')
+            messages.append('Input subtomograms were assumed to be already aligned')
         messages.append('Number of output references: %d' % self.numberOfReferences.get())
         return messages
 
     def _validate(self):
         errors = []
         (Xdim1, Ydim1, Zdim1) = self.inputVolumes.get().getDimensions()
         if Xdim1 != Ydim1 or Ydim1 != Zdim1:
-            errors.append("Input subvolumes are not cubic")
+            errors.append("Input subtomograms are not cubic")
         N0 = -1
         if not self.doGenerateInitial.get():
             if not self.referenceList.hasValue():
                 errors.append("If references are not self generated, you have to provide a reference set of volumes")
             else:
                 (Xdim2, Ydim2, Zdim2) = self.referenceList.get().getDimensions()
                 if Xdim2 != Ydim2 or Ydim2 != Zdim2:
-                    errors.append("Reference subvolumes are not cubic")
+                    errors.append("Reference subtomograms are not cubic")
                 if Xdim1 != Xdim2:
-                    errors.append("Input and reference subvolumes are of different size")
+                    errors.append("Input and reference subtomograms are of different size")
         else:
             N0 = self.numberOfReferences0.get()
         if N0 > 0 and N0 > self.numberOfReferences.get():

xmipptomo/tests/test_protocol_cltomo.py

@@ -0,0 +1,113 @@
+# **************************************************************************
+# *
+# * Authors:    J.L. Vilas ([email protected])
+# *
+# * 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 3 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 '[email protected]'
+# *
+# **************************************************************************
+from pyworkflow.tests import BaseTest, setupTestProject
+from tomo.protocols.protocol_import_coordinates import IMPORT_FROM_EMAN
+import tomo.protocols
+
+from xmipptomo.protocols.protocol_cltomo import XmippProtCLTomo
+from xmipptomo.protocols.protocol_extract_subtomos import XmippProtExtractSubtomos
+
+## Tomogram type constants for particle extraction
+#OUTPUTATTRIBUTE = 'Subtomograms'
+
+class TestXmippProtCLTomoBase(BaseTest):
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+
+    @classmethod
+    def setData(cls, projectData='tomo-em'):
+        from tomo.tests import DataSet
+        cls.dataset = DataSet.getDataSet(projectData)
+        cls.tomogram = cls.dataset.getFile('tomo1')
+        cls.coords3D = cls.dataset.getFile('overview_wbp.txt')
+        cls.coords3D_Large = cls.dataset.getFile('overview_wbp_large.txt')
+        cls.inputSetOfSubTomogram = cls.dataset.getFile('subtomo')
+        cls.smallTomogram = cls.dataset.getFile('coremask_normcorona.mrc')
+
+
+class TestXmippProtCLtomo(TestXmippProtCLTomoBase):
+    """
+    This prepares the protocols to perform the necessary tests.
+    """
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        TestXmippProtCLtomo.setData()
+
+    def _runImportCoordinatesAndTomograms(self):
+        protImportTomogram = self.newProtocol(tomo.protocols.ProtImportTomograms,
+                                              filesPath=self.tomogram,
+                                              samplingRate=5)
+
+        self.launchProtocol(protImportTomogram)
+
+        protImportCoordinates3d = self.newProtocol(tomo.protocols.ProtImportCoordinates3D,
+                                                   auto=IMPORT_FROM_EMAN,
+                                                   filesPath=self.coords3D,
+                                                   importTomograms=protImportTomogram.Tomograms,
+                                                   filesPattern='', boxSize=32,
+                                                   samplingRate=5)
+
+        self.launchProtocol(protImportCoordinates3d)
+        self.assertSetSize(protImportTomogram.Tomograms, 1,
+                           "There was a problem with tomogram output")
+        self.assertSetSize(protImportCoordinates3d.outputCoordinates, 5,
+                           "There was a problem with coordinates 3d output")
+
+        protTomoExtraction = self.newProtocol(XmippProtExtractSubtomos,
+                                                  tomograms=protImportTomogram.Tomograms,
+                                                  coords=protImportCoordinates3d.outputCoordinates,
+                                                  invertContrast=True,
+                                                  boxSize=32)
+
+        self.launchProtocol(protTomoExtraction)
+        self.assertSetSize(getattr(protTomoExtraction, 'Subtomograms'), 5,
+                           "There was a problem with SetOfSubtomogram output")
+
+        return protTomoExtraction
+
+    def _runXmippCLtomo(self):
+        protTomoExtraction = self._runImportCoordinatesAndTomograms()
+        protCLTomo = self.newProtocol(XmippProtCLTomo, inputVolumes=protTomoExtraction.Subtomograms)
+
+        self.launchProtocol(protCLTomo)
+
+
+        return protCLTomo
+
+
+class TestXmippProtCLtomo(TestXmippProtCLtomo):
+    """
+    This class check if CLtomos in Xmipptomo works properly.
+    """
+
+    def test_CLtomo(self):
+        protCLTomo = self._runXmippCLtomo()
+        msg = "There was a problem with CLtomo"
+        self.assertIsNotNone(protCLTomo.outputClasses, msg)
+

xmipptomo/tests/test_protocols_crop.py → xmipptomo/tests/test_protocol_crop.py

@@ -23,11 +23,10 @@
 # *  e-mail address '[email protected]'
 # *
 # **************************************************************************
-from os.path import exists, join, split
+
 from pyworkflow.tests import BaseTest, DataSet, setupTestProject
 from tomo.protocols import ProtImportTomograms
 from xmipptomo.protocols import XmippProtCropTomograms
-from xmipptomo.protocols.protocol_crop_tomograms import SUFIXCROPPED
 
 
 class TestReSizeBase(BaseTest):
@@ -55,16 +54,15 @@ def setUpClass(cls):
         cls.protImportTomos = cls.runImportTomograms(cls.tomos, 16.14)
 
     def testCropTomogramsSamplingRate(self):
-        Rrb = XmippProtCropTomograms()
         crop = self.newProtocol(XmippProtCropTomograms,
-                                    objLabel='crop tomos',
-                                    inputSet=self.protImportTomos.Tomograms,
-                                    xcrop0=100,
-                                    xcropF=900,
-                                    ycrop0=100,
-                                    ycropF=900,
-                                    zcrop0=10,
-                                    zcropF=100)
+                                objLabel='crop tomos',
+                                inputSet=self.protImportTomos.Tomograms,
+                                xcrop0=100,
+                                xcropF=900,
+                                ycrop0=100,
+                                ycropF=900,
+                                zcrop0=10,
+                                zcropF=100)
         self.launchProtocol(crop)
 
         self.assertTrue(crop)

xmipptomo/tests/test_protocols_deep_misalignment_detection.py → xmipptomo/tests/test_protocol_deep_misalignment_detection.py

@@ -24,7 +24,9 @@
 # *
 # *****************************************************************************
 
-from pyworkflow.tests import *
+import os
+
+from pyworkflow.tests import setupTestProject, DataSet, BaseTest
 from tomo.protocols.protocol_import_tomograms import ProtImportTomograms
 from xmipptomo.protocols.protocol_peak_high_contrast import XmippProtPeakHighContrast
 from xmipptomo.protocols.protocol_deep_misalignment_detection import XmippProtDeepDetectMisalignment

xmipptomo/tests/test_protocols_resize.py → xmipptomo/tests/test_protocol_resize.py

@@ -23,12 +23,10 @@
 # *  e-mail address '[email protected]'
 # *
 # **************************************************************************
-from os.path import exists, join, split
+
 from pyworkflow.tests import BaseTest, DataSet, setupTestProject
 from tomo.protocols import ProtImportTomograms
-from xmipptomo.protocols import XmippProtResizeTomograms, XmippProtResizeTiltSeries
-from xmipptomo.protocols.protocol_crop_resize_base import XmippProtResizeBase
-import os
+from xmipptomo.protocols import XmippProtResizeTomograms
 
 
 class TestReSizeBase(BaseTest):
@@ -49,51 +47,49 @@ def runImportTomograms(cls, pattern, samplingRate):
 
 
 class TestReSizeTomograms(TestReSizeBase):
+    _objLabel = 'Resize tomos'
+
     @classmethod
     def setUpClass(cls):
         setupTestProject(cls)
         TestReSizeBase.setData()
         cls.protImportTomos = cls.runImportTomograms(cls.tomos, 16.14)
 
     def testReSizeTomogramsSamplingRate(self):
-        Rrb = XmippProtResizeTomograms()
+        protResizeTomos = XmippProtResizeTomograms()
         reSize = self.newProtocol(XmippProtResizeTomograms,
-                                    objLabel='Resize tomos',
-                                    inputSet=self.protImportTomos.Tomograms,
-                                    resizeOption = Rrb.RESIZE_SAMPLINGRATE,
-                                    resizeSamplingRate = 32.28)
+                                  objLabel=self._objLabel,
+                                  inputSet=self.protImportTomos.Tomograms,
+                                  resizeOption=protResizeTomos.RESIZE_SAMPLINGRATE,
+                                  resizeSamplingRate=32.28)
         self.launchProtocol(reSize)
         self.assertTrue(reSize)
         self.assertSetSize(reSize.outputSetOfTomograms, 2,
                            "resize has failed in the samplingrate option probably related with the use "
                            "of a SetOfTomograms (processing the second tomogram)")
 
-
     def testReSizeTomogramsFactor(self):
-        Rrb = XmippProtResizeTomograms()
+        protResizeTomos = XmippProtResizeTomograms()
         reSize = self.newProtocol(XmippProtResizeTomograms,
-                                    objLabel='Resize tomos',
-                                    inputSet=self.protImportTomos.Tomograms,
-                                    resizeOption = Rrb.RESIZE_FACTOR,
-                                    resizeFactor = 0.5)
+                                  objLabel=self._objLabel,
+                                  inputSet=self.protImportTomos.Tomograms,
+                                  resizeOption=protResizeTomos.RESIZE_FACTOR,
+                                  resizeFactor=0.5)
         self.launchProtocol(reSize)
         self.assertTrue(reSize)
         self.assertSetSize(reSize.outputSetOfTomograms, 2,
                            "resize has failed in the Factor option probably related with the use "
                            "of a SetOfTomograms (processing the second tomogram)")
 
-
     def testReSizeTomogramsPiramid(self):
-        Rrb = XmippProtResizeTomograms()
+        protResizeTomos = XmippProtResizeTomograms()
         reSize = self.newProtocol(XmippProtResizeTomograms,
-                                    objLabel='Resize tomos',
-                                    inputSet=self.protImportTomos.Tomograms,
-                                    resizeOption = Rrb.RESIZE_PYRAMID,
-                                    resizeLevel = 0)
+                                  objLabel=self._objLabel,
+                                  inputSet=self.protImportTomos.Tomograms,
+                                  resizeOption=protResizeTomos.RESIZE_PYRAMID,
+                                  resizeLevel=0)
         self.launchProtocol(reSize)
         self.assertTrue(reSize)
         self.assertSetSize(reSize.outputSetOfTomograms, 2,
                            "Resize has failed in the pyramid option probably related with the use "
                            "of a SetOfTomograms (processing the second tomogram)")
-
-