Merge pull request #166 from I2PC/fi_refactorTest

Fi refactor test

xmipptomo/tests/test_protocols_apply_transform.py

@@ -0,0 +1,64 @@
+# **************************************************************************
+# *
+# * Authors:    Federico P. de Isidro-Gomez
+# *
+# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+from pyworkflow.tests import BaseTest, setupTestProject
+from tomo.tests import DataSet
+
+from xmipptomo.protocols import XmippProtApplyTransformSubtomo, XmippProtPhantomSubtomo
+
+
+class TestXmipptomoApplyTransf(BaseTest):
+    """This class check if the protocol apply_alignment_subtomo works properly."""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        cls.dataset = DataSet.getDataSet('tomo-em')
+
+    def _runPreviousProtocols(self):
+        protPhantom = self.newProtocol(XmippProtPhantomSubtomo, option=1, nsubtomos=5)
+        self.launchProtocol(protPhantom)
+        self.assertIsNotNone(protPhantom.outputSubtomograms,
+                             "There was a problem with subtomograms output")
+        return protPhantom
+
+    def _applyAlignment(self):
+        protPhantom = self._runPreviousProtocols()
+        apply = self.newProtocol(XmippProtApplyTransformSubtomo,
+                                 inputSubtomograms=protPhantom.outputSubtomograms)
+        self.launchProtocol(apply)
+        self.assertIsNotNone(apply.outputSubtomograms,
+                             "There was a problem with subtomograms output")
+        self.assertIsNotNone(apply.outputAverage,
+                             "There was a problem with average output")
+        return apply
+
+    def test_applyAlignment(self):
+        align = self._applyAlignment()
+        self.assertTrue(getattr(align, 'outputSubtomograms'))
+        self.assertTrue(getattr(align, 'outputAverage'))
+        return align

xmipptomo/tests/test_protocols_cc_to_roi.py

@@ -0,0 +1,108 @@
+# **************************************************************************
+# *
+# * Authors:    Federico P. de Isidro-Gomez
+# *
+# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+from pwem.protocols import ProtUnionSet
+from pyworkflow.tests import BaseTest, setupTestProject
+from tomo.tests import DataSet
+from tomo.protocols import (ProtImportCoordinates3D,
+                            ProtImportTomograms,
+                            TomoProtFitEllipsoid)
+
+from xmipptomo.protocols import XmippProtCCroi
+
+
+class TestXmipptomoProtCCtoROI(BaseTest):
+    """ This class check if the protocol connected components to ROIs works properly."""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        cls.dataset = DataSet.getDataSet('tomo-em')
+        cls.tomogram = cls.dataset.getFile('tomo1')
+        cls.coords3D = cls.dataset.getFile('overview_wbp.txt')
+
+    def _runPreviousProtocols(self):
+        protImportTomogram = self.newProtocol(ProtImportTomograms,
+                                              filesPath=self.tomogram,
+                                              samplingRate=5)
+        self.launchProtocol(protImportTomogram)
+        self.assertIsNotNone(protImportTomogram.Tomograms,
+                             "There was a problem with tomogram output")
+
+        protImportCoordinates3d = self.newProtocol(ProtImportCoordinates3D,
+                                                   filesPath=self.coords3D,
+                                                   importTomograms=protImportTomogram.Tomograms,
+                                                   boxSize=32,
+                                                   samplingRate=5)
+        self.launchProtocol(protImportCoordinates3d)
+        self.assertIsNotNone(protImportCoordinates3d.outputCoordinates,
+                             "There was a problem with coordinates 3d output")
+
+        protImportCoordinates3dBis = self.newProtocol(ProtImportCoordinates3D,
+                                                      filesPath=self.coords3D,
+                                                      importTomograms=protImportTomogram.Tomograms,
+                                                      boxSize=32,
+                                                      samplingRate=5)
+        self.launchProtocol(protImportCoordinates3dBis)
+        self.assertIsNotNone(protImportCoordinates3dBis.outputCoordinates,
+                             "There was a problem with coordinates 3d output 2")
+
+        protJoinCoordinates = self.newProtocol(ProtUnionSet,
+                                               inputSets=[protImportCoordinates3d.outputCoordinates,
+                                                          protImportCoordinates3dBis.outputCoordinates])
+        self.launchProtocol(protJoinCoordinates)
+        self.assertIsNotNone(protJoinCoordinates.outputSet,
+                             "There was a problem with join coordinates output")
+
+        protFitVesicles = self.newProtocol(TomoProtFitEllipsoid,
+                                           input=protJoinCoordinates.outputSet,
+                                           inputTomos=protImportTomogram.Tomograms)
+        self.launchProtocol(protFitVesicles)
+        self.assertIsNotNone(protFitVesicles.outputMeshes, "There was a problem with output vesicles (SetOfMeshes)")
+        return protFitVesicles, protJoinCoordinates
+
+    def test_CCtoROIs(self):
+        protFitVesicles, protJoinCoordinates = self._runPreviousProtocols()
+        protCCtoROI = self.newProtocol(XmippProtCCroi,
+                                       inputCoordinates=protJoinCoordinates.outputSet,
+                                       inputMeshes=protFitVesicles.outputMeshes)
+        self.launchProtocol(protCCtoROI)
+        self.assertIsNotNone(protCCtoROI.outputSet, "There was a problem with CCtoROIs output")
+        self.assertEqual(protCCtoROI.outputSet.getSize(), 10)
+        self.assertEqual(protCCtoROI.outputSet.getBoxSize(), 32)
+        return protCCtoROI
+
+    def test_CCtoROIsPoints(self):
+        protFitVesicles, protJoinCoordinates = self._runPreviousProtocols()
+        protCCtoROI = self.newProtocol(XmippProtCCroi,
+                                       inputCoordinates=protJoinCoordinates.outputSet,
+                                       inputMeshes=protFitVesicles.outputMeshes,
+                                       selection=1)
+        self.launchProtocol(protCCtoROI)
+        self.assertIsNotNone(protCCtoROI.outputSet, "There was a problem with CCtoROIs points output")
+        self.assertEqual(protCCtoROI.outputSet.getSize(), 10)
+        self.assertEqual(protCCtoROI.outputSet.getBoxSize(), 32)

xmipptomo/tests/test_protocols_conected_components.py

@@ -0,0 +1,61 @@
+# **************************************************************************
+# *
+# * Authors:    Federico P. de Isidro-Gomez
+# *
+# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+from pyworkflow.tests import BaseTest, setupTestProject
+
+from tomo.tests import DataSet
+from tomo.protocols import (ProtImportCoordinates3D,
+                            ProtImportTomograms)
+
+
+class TestXmipptomoProtCC(BaseTest):
+    """ This class check if the protocol to compute connected components works
+    properly."""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        cls.dataset = DataSet.getDataSet('tomo-em')
+        cls.tomogram = cls.dataset.getFile('tomo1')
+        cls.coords3D = cls.dataset.getFile('overview_wbp.txt')
+
+    def _runPreviousProtocols(self):
+        protImportTomogram = self.newProtocol(ProtImportTomograms,
+                                              filesPath=self.tomogram,
+                                              samplingRate=5)
+        self.launchProtocol(protImportTomogram)
+        protImportCoordinates3d = self.newProtocol(ProtImportCoordinates3D,
+                                                   filesPath=self.coords3D,
+                                                   importTomograms=protImportTomogram.Tomograms,
+                                                   boxSize=32,
+                                                   samplingRate=5)
+        self.launchProtocol(protImportCoordinates3d)
+        self.assertIsNotNone(protImportTomogram.Tomograms,
+                             "There was a problem with tomogram output")
+        self.assertIsNotNone(protImportCoordinates3d.outputCoordinates,
+                             "There was a problem with coordinates 3d output")
+        return protImportCoordinates3d

xmipptomo/tests/test_protocols_half_maps.py

@@ -0,0 +1,65 @@
+# **************************************************************************
+# *
+# * Authors:    Federico P. de Isidro-Gomez
+# *
+# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+import numpy as np
+
+from pwem.emlib.image import ImageHandler
+from pyworkflow.tests import BaseTest, setupTestProject
+
+from xmipptomo.protocols import XmippProtPhantomSubtomo, XmippProtHalfMapsSubtomo
+
+
+class TestXmipptomoHalfMaps(BaseTest):
+    """This class check if the protocol to create half maps from a SetOfSubtomograms
+    works properly"""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+
+    def _phantom(self):
+        phantom = self.newProtocol(XmippProtPhantomSubtomo, option=1)
+        self.launchProtocol(phantom)
+        self.assertIsNotNone(phantom.outputSubtomograms,
+                             "There was a problem with subtomograms output")
+        return phantom
+
+    def _half_maps(self, subtomos):
+        halfMaps = self.newProtocol(XmippProtHalfMapsSubtomo, inputSubtomograms=subtomos)
+        self.launchProtocol(halfMaps)
+        self.assertIsNotNone(halfMaps.halfMaps,
+                             "There was a problem with half maps output")
+        return halfMaps
+
+    def test_half_maps(self):
+        phantom = self._phantom()
+        halfMaps = self._half_maps(phantom.outputSubtomograms)
+        mapEven = np.squeeze(ImageHandler().read(halfMaps.halfMaps[1].getFileName()).getData())
+        mapOdd = np.squeeze(ImageHandler().read(halfMaps.halfMaps[2].getFileName()).getData())
+        error = np.sqrt(np.sum((mapEven - mapOdd) ** 2) / mapEven.size)
+        self.assertAlmostEqual(error, 0.0, delta=0.1, msg="Unexpected half maps")
+        return halfMaps

xmipptomo/tests/test_protocols_mapback.py

@@ -0,0 +1,78 @@
+# **************************************************************************
+# *
+# * Authors:    Federico P. de Isidro-Gomez
+# *
+# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+from pyworkflow.tests import BaseTest, setupTestProject
+
+from tomo.tests import DataSet
+from tomo.protocols import ProtImportTomograms
+
+from xmipptomo.protocols import XmippProtSubtomoMapBack, XmippProtPhantomSubtomo
+
+
+class TestXmipptomoMapback(BaseTest):
+    """This class check if the protocol mapback works properly."""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        cls.dataset = DataSet.getDataSet('tomo-em')
+        cls.tomogram = cls.dataset.getFile('tomo1')
+        cls.coords3D = cls.dataset.getFile('overview_wbp.txt')
+
+    def _runPreviousProtocols(self):
+        protImportTomogram = self.newProtocol(ProtImportTomograms,
+                                              filesPath=self.tomogram,
+                                              samplingRate=5)
+        self.launchProtocol(protImportTomogram)
+        self.assertIsNotNone(protImportTomogram.Tomograms,
+                             "There was a problem with tomogram output")
+
+        protPhantom = self.newProtocol(XmippProtPhantomSubtomo,
+                                       option=1,
+                                       sampling=4,
+                                       nsubtomos=5,
+                                       coords=True,
+                                       tomos=protImportTomogram.Tomograms)
+        self.launchProtocol(protPhantom)
+        self.assertIsNotNone(protPhantom.outputSubtomograms,
+                             "There was a problem with subtomograms output")
+
+        return protImportTomogram, protPhantom
+
+    def test_mapback(self):
+        _, protPhantom = self._runPreviousProtocols()
+        mapback = self.newProtocol(XmippProtSubtomoMapBack,
+                                   selection=1,
+                                   inputSubtomos=protPhantom.outputSubtomograms,
+                                   inputRef=protPhantom,
+                                   removeBackground=True)
+
+        mapback.inputRef.setExtended("outputSubtomograms.1")
+        self.launchProtocol(mapback)
+
+        self.assertSetSize(getattr(mapback, XmippProtSubtomoMapBack._possibleOutputs.tomograms.name), 1,
+                           "There was a problem with tomograms output")