Merge pull request #3 from scipion-em/fix/viewer_tomograms

Implement viewer for import tomograms

tomo/viewers/__init__.py

@@ -25,4 +25,5 @@
 # **************************************************************************
 
 from .viewers_data import TomoDataViewer
-from .viewer_imod import ImodViewer, ImodObjectView
+from .viewer_imod import ImodViewer, ImodObjectView
+from .viewer_tomograms import ViewerProtImportTomograms

tomo/viewers/viewer_tomograms.py

@@ -0,0 +1,152 @@
+# **************************************************************************
+# *
+# * Authors:     Adrian Quintana (adrian@eyeseetea.com) [1]
+# *
+# * [1] EyeSeeTea Ltd, London, UK
+# *
+# * 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'
+# *
+# **************************************************************************
+
+
+"""
+This module implements visualization program
+for input tomograms.
+"""
+
+import os
+from distutils.spawn import find_executable
+
+import pyworkflow.protocol.params as params
+from pyworkflow.em.convert import ImageHandler
+from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO, ProtocolViewer
+import pyworkflow.em.viewers as viewers
+
+from tomo.protocols import ProtImportTomograms
+
+TOMOGRAM_SLICES = 1
+TOMOGRAM_CHIMERA = 0
+
+
+class ViewerProtImportTomograms(ProtocolViewer):
+    """ Wrapper to visualize different type of objects
+    with the Xmipp program xmipp_showj. """
+
+    _label = 'viewer input tomogram'
+    _targets = [ProtImportTomograms]
+    _environments = [DESKTOP_TKINTER, WEB_DJANGO]
+
+    def _defineParams(self, form):
+        form.addSection(label='Visualization of input tomograms')
+        form.addParam('displayTomo', params.EnumParam,
+                      choices=['chimera', 'slices'],
+                      default=TOMOGRAM_CHIMERA,
+                      display=params.EnumParam.DISPLAY_HLIST,
+                      label='Display tomogram with',
+                      help='*chimera*: display tomograms as surface with '
+                           'Chimera.\n *slices*: display tomograms as 2D slices '
+                           'along z axis.\n If number of tomograms == 1, '
+                           'a system of coordinates is shown'
+                      )
+
+    def _getVisualizeDict(self):
+        return {
+            'displayTomo': self._showTomograms,
+        }
+
+    def _validate(self):
+        if (self.displayTomo == TOMOGRAM_CHIMERA
+                and find_executable(viewers.viewer_chimera.Chimera.getProgram()) is None):
+            return ["chimera is not available. "
+                    "Either install it or choose option 'slices'. "]
+        return []
+
+    # =========================================================================
+    # ShowTomograms
+    # =========================================================================
+
+    def _showTomograms(self, paramName=None):
+        if self.displayTomo == TOMOGRAM_CHIMERA:
+            return self._showTomogramsChimera()
+
+        elif self.displayTomo == TOMOGRAM_SLICES:
+            return self._showTomogramsSlices()
+
+    def _createSetOfTomograms(self):
+        try:
+            setOfTomograms = self.protocol.outputTomograms
+            sampling = self.protocol.outputTomograms.getSamplingRate()
+        except:
+            setOfTomograms = self.protocol._createSetOfTomograms()
+            setOfTomograms.append(self.protocol.outputTomogram)
+            sampling = self.protocol.outputTomogram.getSamplingRate()
+
+        return sampling, setOfTomograms
+
+    def _showTomogramsChimera(self):
+        """ Create a chimera script to visualize selected tomograms. """
+        tmpFileNameCMD = self.protocol._getTmpPath("chimera.cmd")
+        f = open(tmpFileNameCMD, "w")
+        sampling, _setOfTomograms = self._createSetOfTomograms()
+        count = 0  # first model in chimera is a tomogram
+
+        if len(_setOfTomograms) == 1:
+            count = 1  # first model in chimera is the bild file
+            # if we have a single tomogram then create axis
+            # as bild file. Chimera must read the bild file first
+            # otherwise system of coordinates will not
+            # be in the center of the window
+
+            dim = self.protocol.outputTomogram.getDim()[0]
+            tmpFileNameBILD = os.path.abspath(self.protocol._getTmpPath(
+                "axis.bild"))
+            viewers.viewer_chimera.Chimera.createCoordinateAxisFile(dim,
+                                                                    bildFileName=tmpFileNameBILD,
+                                                                    sampling=sampling)
+            f.write("open %s\n" % tmpFileNameBILD)
+            f.write("cofr 0,0,0\n")  # set center of coordinates
+            count = 1  # skip first model because is not a 3D map
+
+        for tomo in _setOfTomograms:
+            localTomo = os.path.abspath(ImageHandler.removeFileType(
+                tomo.getFileName()))
+            if localTomo.endswith("stk"):
+                self.showError("Extension .stk is not supported")
+            f.write("open %s\n" % localTomo)
+            f.write("volume#%d style surface voxelSize %f\n" %
+                    (count, sampling))
+            count += 1
+
+        if len(_setOfTomograms) > 1:
+            f.write('tile\n')
+        else:
+            x, y, z = tomo.getShiftsFromOrigin()
+            f.write("volume#1 origin %0.2f,%0.2f,%0.2f\n" % (x, y, z))
+        f.close()
+        return [viewers.viewer_chimera.ChimeraView(tmpFileNameCMD)]
+
+    def _showTomogramsSlices(self):
+        # Write an sqlite with all tomograms selected for visualization.
+        sampling, setOfTomograms = self._createSetOfTomograms()
+
+        if len(setOfTomograms) == 1:
+            return [self.objectView(self.protocol.outputTomogram)]
+
+        return [self.objectView(setOfTomograms)]
+