Merge pull request #184 from I2PC/legacy

Adding protocols to legacy

xmipptomo/legacy/tests/test_protocol_score_transform.py

@@ -0,0 +1,71 @@
+# **************************************************************************
+# *
+# * 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 pyworkflow.tests import BaseTest, setupTestProject
+from tomo.tests import DataSet
+
+from xmipptomo.protocols import XmippProtScoreTransform
+from tomo.protocols import ProtImportSubTomograms
+
+class TestXmippTomoScoreTransform(BaseTest):
+    """This class check if the protocol score_transform works properly."""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        cls.dataset = DataSet.getDataSet('tomo-em')
+        cls.setOfSubtomograms = cls.dataset.getFile('basename.hdf')
+
+    def _runImportSubtomos(self, label):
+        protImport = self.newProtocol(ProtImportSubTomograms,
+                                      filesPath=self.setOfSubtomograms,
+                                      samplingRate=5,
+                                      label=label)
+        self.launchProtocol(protImport)
+        self.assertIsNotNone(protImport.outputSubTomograms,
+                             "There was a problem with import subtomograms output")
+        return protImport.outputSubTomograms
+
+    def _scoreTransformations(self, firstSubtomos, secondSubtomos):
+        scoredTr = self.newProtocol(XmippProtScoreTransform,
+                                   firstSubtomos=firstSubtomos,
+                                   secondSubtomos=secondSubtomos,
+                                   label='Score Subtomogram Transformations')
+        self.launchProtocol(scoredTr)
+        self.assertIsNotNone(scoredTr.outputSetOfSubtomogram,
+                             "There was a problem with score subtomograms output")
+        return scoredTr.outputSetOfSubtomogram
+
+    def test_scoreTransformations(self):
+        firstSubtomos = self._runImportSubtomos('First Subtomograms')
+        secondSubtomos = self._runImportSubtomos('Second Subtomograms')
+        scoredSubtomos = self._scoreTransformations(firstSubtomos, secondSubtomos)
+        self.assertTrue(scoredSubtomos.getSize() == 4)
+        dist = scoredSubtomos.aggregate(["MAX"], "distanceScore", ["distanceScore"])
+        dist = np.asarray([d["distanceScore"] for d in dist])
+        meanDist = np.mean(dist)
+        self.assertTrue(meanDist == 0)
+        return scoredSubtomos

xmipptomo/protocols/__init__.py

@@ -35,7 +35,6 @@
 from .protocol_dose_filter import XmippProtDoseFilter
 from .protocol_filter_coordinates_by_map import XmippProtFilterCoordinatesByMap
 from .protocol_crop_tomograms import XmippProtCropTomograms
-from .protocol_denoising_confidence import XmippProtConfTomo
 from .protocol_extract_particlestacks import XmippProtExtractParticleStacks
 from .protocol_extract_subtomos import XmippProtExtractSubtomos
 from .protocol_flexalign import XmippProtTsFlexAlign
@@ -49,7 +48,6 @@
 from .protocol_resolution_local_monotomo import XmippProtMonoTomo
 from .protocol_roiIJ import XmippProtRoiIJ
 from .protocol_score_coordinates import XmippProtScoreCoordinates
-from .protocol_score_transform import XmippProtScoreTransform
 from .protocol_splitTS import XmippProtSplitTiltSeries
 from .protocol_subtraction_subtomo import XmippProtSubtractionSubtomo
 from .protocol_subtomo_map_back import XmippProtSubtomoMapBack

xmipptomo/viewers/__init__.py

@@ -27,5 +27,4 @@
 from .viewer_cltomo import XmippCLTomoViewer, XmippProtTsFlexAlignViewer
 from .viewer_resolution_local_monotomo import XmippMonoTomoViewer
 from .viewer_phantom_create import XmippPhantomSubtomoViewer
-from .viewer_score_subtomos import XmippTomoScoreSubtomoViewer