Merge branch 'devel' into tests

Author: martin-s-a

xmipptomo/protocols/protocol_phantom_subtomo.py

@@ -35,6 +35,7 @@
 from pyworkflow.protocol.params import LEVEL_ADVANCED,IntParam, FloatParam, EnumParam, PointerParam, TextParam, BooleanParam
 from tomo.protocols import ProtTomoBase
 from tomo.objects import SetOfSubTomograms, SubTomogram, TomoAcquisition, Coordinate3D, SetOfCoordinates3D
+from pwem.objects import Acquisition, Volume
 
 import tomo.constants as const
 from pwem.convert.headers import setMRCSamplingRate
@@ -181,13 +182,13 @@ def _defineParams(self, form):
         lineStat.addParam('meanNoise', IntParam, label='mean', default=0, condition='not differentStatistics')
         lineStat.addParam('stdNoise', IntParam, label='std', default=40, condition='not differentStatistics')
 
+
     # --------------------------- INSERT steps functions --------------------------------------------
     def _insertAllSteps(self):
 
         #NOTE: This protocol was discussed with the ScipionTeam about if the subtomograms have or do not have tomogramId.
         # The agreement was that the tomogramId should not appear if subtomograms are imported or phantoms created
         self._insertFunctionStep(self.createSubtomogramsStep)
-        self._insertFunctionStep(self.createOutputStep)
 
     # --------------------------- STEPS functions --------------------------------------------
     def createSubtomogramsStep(self):
@@ -197,24 +198,38 @@ def createPhantomSubtomograms(self):
         if self.mwfilter.get():
             mwangle = self.mwangle.get()
         else:
-            mwangle = 90
+            mwangle = 90.0
 
         fnInVol = None
         dim = None
         if self.option == 0:
             inputVol = self.inputVolume.get()
             fnInVol = inputVol.getFileName()
             dim = inputVol.getDim()
+            fnRef = self.inputVolume.get().getFileName()
         if self.option == 1:
             dim, fnInVol = self.createGeometricalPhantom()
+            fnRef = self._getExtraPath(FN_PHANTOM+MRC_EXT)
+        
+        if self.nsubtomos.get() == 1:
+            volume = Volume()
+            volume.setFileName(fnRef)
+            volume.setSamplingRate(self.sampling.get())
+            self._defineOutputs(outputVolume=volume)
+            if self.option.get() == 0:
+                self._defineSourceRelation(self.inputVolume.get(), volume)
+        else:
+            self.definingOrientationsAndRegisteringInformation(dim, mwangle, fnInVol)
+            self.createOutputStep()
 
-        self.definingOrientationsAndRegisteringInformation(dim, mwangle, fnInVol)
 
     def definingOrientationsAndRegisteringInformation(self, dim, mwangle, fnVol):
+        
+        numberOfSubtomos = self.nsubtomos.get()
         self.createOutputSet(dim)
+
         tomo = None
-        coordsBool = self.generateCoordinates()
-        if coordsBool:
+        if self.generateCoordinates():
             tomos = self.tomos.get()
             tomo = tomos.getFirstItem()
             self.coordsSet = self._createSetOfCoordinates3D(tomos)
@@ -228,11 +243,21 @@ def definingOrientationsAndRegisteringInformation(self, dim, mwangle, fnVol):
         acq = TomoAcquisition()
         acq.setAngleMax(mwangle)
         acq.setAngleMin(mwangle * -1)
+        acq.setStep(3.0)
+        acq.setAccumDose(100.0)
+        acq.setDosePerFrame(3.0)
+        acq.setTiltAxisAngle(0.0)
+
+        acq.setAmplitudeContrast(0.1)
+        acq.setSphericalAberration(2.7)
+        acq.setVoltage(300)
+        acq.setMagnification(50000)
+
 
         if self.randomseed.get():
             np.random.seed(42)
 
-        for i in range(int(self.nsubtomos.get())):
+        for i in range(int(numberOfSubtomos)):
             fnPhantomi = self._getExtraPath(FN_PHANTOM + str(int(i+1)) + MRC_EXT)
 
             if self.addNoise.get():
@@ -254,6 +279,7 @@ def definingOrientationsAndRegisteringInformation(self, dim, mwangle, fnVol):
             # Add the subtomogram and the coordinate if applies
             self._addSubtomogram(tomo, acq, fn_aux, rot, tilt, psi, shiftX, shiftY, shiftZ)
 
+
     def createGeometricalPhantom(self):
         fnVol = self._getExtraPath(FN_PHANTOM+MRC_EXT)
         desc = self.create.get()
@@ -374,6 +400,7 @@ def createOutputSet(self, dim):
         self.outputSet.setDim(dim)
         self.outputSet.setSamplingRate(self.sampling.get())
 
+
     def _addSubtomogram(self, tomo, acq, phantomfn, rot, tilt, psi, shiftX, shiftY, shiftZ):
         """ Creates and adds a the phantom subtomogram to the set. It creates the coordinate as well if active"""
         subtomo = SubTomogram()
@@ -389,6 +416,7 @@ def _addSubtomogram(self, tomo, acq, phantomfn, rot, tilt, psi, shiftX, shiftY,
         subtomo.phantom_shiftX = Integer(shiftX)
         subtomo.phantom_shiftY = Integer(shiftY)
         subtomo.phantom_shiftZ = Integer(shiftZ)
+        
 
         # Scipion alignment matrix
         A = euler_matrix(np.deg2rad(psi), np.deg2rad(tilt), np.deg2rad(rot), 'szyz')
@@ -419,6 +447,7 @@ def _addCoordinate(self, subtomo, tomo):
             coor.setX(rng.integers(tomoDim[0]), const.BOTTOM_LEFT_CORNER)
             coor.setY(rng.integers(tomoDim[1]), const.BOTTOM_LEFT_CORNER)
             coor.setZ(rng.integers(tomoDim[2]), const.BOTTOM_LEFT_CORNER)
+            coor.setVolId(1)
 
             self.coordsSet.append(coor)
             self.coordsSet.setBoxSize(subtomo.getDim()[0])

xmipptomo/protocols/protocol_resolution_local_monotomo.py

@@ -38,6 +38,7 @@
 from pwem.emlib.image import ImageHandler
 import pwem.emlib.metadata as md
 from pwem.protocols import EMProtocol
+from pyworkflow import utils as pwutils
 
 from tomo.protocols import ProtTomoBase
 from tomo.objects import Tomogram
@@ -120,7 +121,7 @@ def _defineParams(self, form):
 
         line.addParam('minRes', FloatParam, default=0, label='High')
         line.addParam('maxRes', FloatParam, allowsNull=True, label='Low')
-        line.addParam('stepSize', FloatParam, allowsNull=True, default=0.5,
+        line.addParam('stepSize', FloatParam, allowsNull=True, default=1.0,
                       expertLevel=LEVEL_ADVANCED, label='Step')
 
         form.addParallelSection(threads=4, mpi=0)
@@ -179,7 +180,8 @@ def resolutionMonoTomoStep(self, tomId):
 
         # Defining the output folder
         tomoPath = self._getExtraPath(tsId)
-        os.mkdir(tomoPath)
+
+        pwutils.path.makePath(tomoPath)
 
         # Defining outfiles
         outputlocalResTomoFn = self.createOutputPath(TOMOGRAM_RESOLUTION_FILE, tsId, MRCEXT)

xmipptomo/protocols/protocol_subtraction_subtomo.py

@@ -26,12 +26,16 @@
 # *
 # **************************************************************************
 
-from pyworkflow import BETA, UPDATED, NEW, PROD
+from pyworkflow import UPDATED
 from pyworkflow.protocol.params import PointerParam, BooleanParam, IntParam, FloatParam
 from pyworkflow.protocol.constants import LEVEL_ADVANCED
 from pwem.protocols import EMProtocol
+from pwem.objects import Volume
 from pwem.constants import ALIGN_3D
 from tomo.protocols import ProtTomoBase
+from tomo.objects import SetOfSubTomograms, SubTomogram
+import pwem.emlib.metadata as md
+from pwem.emlib import lib
 from xmipptomo.convert import writeSetOfSubtomograms, readSetOfSubtomograms
 
 OUTPUT = "output_subtomograms.xmd"
@@ -51,7 +55,7 @@ def _defineParams(self, form):
         form.addSection(label='Input')
         form.addParam('inputSubtomos', PointerParam, pointerClass='SetOfSubTomograms', label="Subtomograms ",
                       help='Select the SetOfSubTomograms with transform matrix which will be subtracted.')
-        form.addParam('average', PointerParam, pointerClass='SubTomogram', label="Average subtomogram ",
+        form.addParam('average', PointerParam, pointerClass='Volume', label="Average subtomogram ",
                       help='Select an average subtomogram to be subtracted.')
         form.addParam('maskBool', BooleanParam, label='Mask subtomograms?', default=True,
                       help='The mask are not mandatory but highly recommendable.')
@@ -79,9 +83,9 @@ def _defineParams(self, form):
 
     # --------------------------- INSERT steps functions --------------------------------------------
     def _insertAllSteps(self):
-        self._insertFunctionStep('convertStep')
-        self._insertFunctionStep('subtractionStep')
-        self._insertFunctionStep('createOutputStep')
+        self._insertFunctionStep(self.convertStep)
+        self._insertFunctionStep(self.subtractionStep)
+        self._insertFunctionStep(self.createOutputStep)
 
     # --------------------------- STEPS functions --------------------------------------------
     def convertStep(self):
@@ -114,7 +118,19 @@ def createOutputStep(self):
         inputSubtomos = self.inputSubtomos.get()
         outputSet = self._createSetOfSubTomograms()
         outputSet.copyInfo(inputSubtomos)
-        readSetOfSubtomograms(self._getExtraPath(OUTPUT), outputSet, alignType=ALIGN_3D)
+        sampling = self.average.get().getSamplingRate()
+        #readSetOfSubtomograms(self._getExtraPath(OUTPUT), outputSet, alignType=ALIGN_3D)
+        
+        mdsubtomos = lib.MetaData(self._getExtraPath(OUTPUT))
+
+        for row in md.iterRows(mdsubtomos):
+            idx = row.getValue(md.MDL_PARTICLE_ID)
+            subtomo = SubTomogram(objId=idx)
+            fn = row.getValue(md.MDL_IMAGE)
+            subtomo.setFileName(fn)
+            subtomo.setSamplingRate(sampling)
+            outputSet.append(subtomo)
+
         self._defineOutputs(outputSubtomograms=outputSet)
         self._defineSourceRelation(inputSubtomos, outputSet)
 

xmipptomo/tests/test_protocol_monotomo.py

@@ -64,16 +64,13 @@ def testMonoTomo(self):
                                     useMask=False,
                                     minRes=1,
                                     maxRes=150,
+                                    stepSize = 5.0
                                     )
         self.launchProtocol(MonoTomo)
-        self.assertTrue(exists(MonoTomo._getExtraPath('odd_tomogram_rx1/fullTomogram_odd_tomogram_rx1.mrc')),
-                        "MonoTomo has failed creating the resolution tomogram")
         self.assertTrue(exists(MonoTomo._getExtraPath('odd_tomogram_rx1/histogram_resolution_odd_tomogram_rx1.xmd')),
                         "MonoTomo has failed creating the resolution histogram")
         self.assertTrue(exists(MonoTomo._getExtraPath('odd_tomogram_rx1/localResolutionTomogram_odd_tomogram_rx1.mrc')),
                         "MonoTomo has failed creating the mean tomogram")
-        self.assertTrue(exists(MonoTomo._getExtraPath('odd_tomogram_rx2/fullTomogram_odd_tomogram_rx2.mrc')),
-                        "MonoTomo has failed creating the resolution tomogram")
         self.assertTrue(exists(MonoTomo._getExtraPath('odd_tomogram_rx2/histogram_resolution_odd_tomogram_rx2.xmd')),
                         "MonoTomo has failed creating the resolution histogram")
         self.assertTrue(exists(MonoTomo._getExtraPath('odd_tomogram_rx2/localResolutionTomogram_odd_tomogram_rx2.mrc')),

xmipptomo/tests/test_protocol_subtraction_subtomo.py

@@ -42,7 +42,7 @@ def _runPreviousProtocols(self):
                                          option=1,
                                          nsubtomos=1)
         self.launchProtocol(createAverage)
-        self.assertIsNotNone(createAverage.outputSubtomograms,
+        self.assertIsNotNone(createAverage.outputVolume,
                              "There was a problem with subtomogram average phantom output")
         createSubtomos = self.newProtocol(XmippProtPhantomSubtomo,
                                           option=1,
@@ -58,7 +58,7 @@ def test_subtraction(self):
         createAverage, createSubtomos = self._runPreviousProtocols()
         subtraction = self.newProtocol(XmippProtSubtractionSubtomo,
                                        inputSubtomos=createSubtomos.outputSubtomograms,
-                                       average=createAverage.outputSubtomograms,
+                                       average=createAverage.outputVolume,
                                        maskBool=False)
         self.launchProtocol(subtraction)
         self.assertIsNotNone(subtraction.outputSubtomograms,