def _showOriginalVolumeSlices(self, param=None):
if self.protocol.halfVolumes.get() is True:
cm = DataView(self.protocol.inputVolume.get().getFileName())
cm2 = DataView(self.protocol.inputVolume2.get().getFileName())
return [cm, cm2]
else:
cm = DataView(self.protocol.inputVolumes.get().getFileName())
return [cm]
def _viewParam(self, param=None):
if param == 'doShowLog':
view = self.textView([self.protocol.getOutputLog()],
"Output log file")
elif param == 'doShowAmp':
view = DataView(self.protocol.getOutputAmplitudes())
elif param == 'doShowAmpRot':
view = DataView(self.protocol.getOutputAmplitudesRot())
elif param == 'doShowAmpCorr':
view = DataView(self.protocol.getOutputAmplitudesCorr())
return [view]
def _viewParam(self, param=None):
if param == 'doShowEigenImages':
view = DataView(self.protocol.getOutputEigenImages())
elif param == 'doShowEigPixImages':
view = DataView(self.protocol._getFileName('msa_eigen_pixel'))
elif param == 'doShowPixelVecCoordImages':
view = DataView(self.protocol._getFileName('msa_pixvec_coord'))
elif param == 'doShowMsaLisFile':
view = self.textView([self.protocol.getOutputLis()],
"MSA lis file")
elif param == 'doShowMsaPltFile':
view = self.textView([self.protocol.getOutputPlt()],
"MSA plt file")
return [view]
def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path)
else os.path.join(os.getcwd(), path))
subprocess.Popen([pw.getScipionScript(), 'view', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
import xmippLib
fn = xmippLib.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewers import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def _visualize(self, obj, **args):
if hasattr(obj, 'outputVolumes'):
XmippViewer._visualize(self, self.protocol.outputVolumes)
fnBasis = self.protocol._getExtraPath('split_pc1.vol')
if exists(fnBasis):
self._views.append(DataView(fnBasis))
return self._views
def _showInternalParticles(self, paramName=None):
views = []
for it in self._iterations:
fnDir = self.protocol._getExtraPath("Iter%03d" % it)
fnAngles = join(fnDir, "angles.xmd")
if exists(fnAngles):
views.append(
DataView(fnAngles, viewParams={showj.MODE: showj.MODE_MD}))
return views
def _viewVolume(self, e=None):
import pyworkflow.em.metadata as md
viewLabels = 'id enabled _index _filename _xmipp_weight'
cm = DataView(self.protocol.outputVolumes.getFileName(),
viewParams={
MODE: MODE_MD,
ORDER: viewLabels,
RENDER: '_filename',
VISIBLE: viewLabels
})
return [cm]
def _visualize(self, obj, **kwargs):
views = []
outputClasses = getattr(obj, 'outputClasses', None)
if outputClasses is not None:
renderLabels = '_representative._filename _reprojection._filename'
labels = 'id enabled %s _representative._xmipp_angleRot _representative._xmipp_angleTilt _representative._xmipp_classCount' % renderLabels
views.append(
ObjectView(self._project,
outputClasses.strId(),
outputClasses.getFileName(),
viewParams={
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.RENDER: renderLabels,
showj.MODE: showj.MODE_MD
}))
# outputAverages = getattr(obj, 'outputAverages', None)
# if outputAverages is not None:
# renderLabels = '_filename'
# labels = 'id enabled %s _xmipp_angleRot _xmipp_angleTilt _xmipp_classCount' % renderLabels
# views.append(ObjectView(self._project, outputAverages.strId(),
# outputAverages.getFileName(),
# viewParams={showj.ORDER: labels,
# showj.VISIBLE: labels,
# showj.RENDER: renderLabels,
# showj.MODE: showj.MODE_MD}))
if hasattr(obj, 'outputVolumes'):
outputVolumes = obj.outputVolumes
labels = 'id enabled comment _filename '
views.append(
ObjectView(self._project,
outputVolumes.strId(),
outputVolumes.getFileName(),
viewParams={
showj.MODE: showj.MODE_MD,
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.RENDER: '_filename'
}))
fnBasis = self.protocol._getExtraPath('split_pc1.vol')
if exists(fnBasis):
views.append(DataView(fnBasis))
return views
def _showPlot(self, paramName=None):
views = []
color = self.colozaxis
rmax = self.radcut.get()
if self.displayPlot == TILT_SCATTER:
views.append(self._createScatterPlot(rmax, colorzaxis=color))
elif self.displayPlot == TILT_CONTOUR:
plotFn = self.protocol._getFileName('outputContourPlot')
if pwutils.exists(plotFn):
views.append(DataView(plotFn))
else:
raise Exception("Contour plot file not found: %s" % plotFn)
return views
def _viewP(self, e=None):
volId = int(self.volForCurve.get())
vol = self.protocol.outputVolumes[volId]
if vol is None: # Wrong volume selection
return [self.errorMessage("Invalid volume id *%d*" % volId)]
pFn = vol.clusterMd.get()
mdCls = md.MetaData(vol.clusterMd.get())
return [
self._viewPlot("Cluster tendency parameter for each image",
IMAGE_INDEX,
P_INDEX,
mdCls,
md.MDL_IMAGE_IDX,
md.MDL_WEIGHT,
color='b'),
DataView(pFn)
]
def showExtraFile(volumeSet, volId, suffix):
vol = volumeSet[volId]
volFn = vol.getFileName().replace('.hdf', suffix)
DataView(volFn).show()
def _showOriginalVolumeSlices(self, param=None):
cm = DataView(self.protocol.inputVolume.get().getFileName())
return [cm]
def _showVolumeSlices(self, param=None):
cm = DataView(self.protocol.resolution_Volume.getFileName())
return [cm]
def getFileActions(self, objFile):
from pyworkflow.em.viewers import DataView
fn = objFile.getPath()
return [('Open with Xmipp viewer', lambda: DataView(fn).show(),
Icon.ACTION_VISUALIZE)]
def _showDoASlices(self, param=None):
cm = DataView(self.protocol._getExtraPath(OUTPUT_DOA_FILE))
return [cm]
def _viewInfo(self, fn):
""" Display the info block in the metadata for a level convergence. """
return DataView('info@' + fn)
def createDataView(self, filename, viewParams={}):
return DataView(filename, env=self._env, viewParams=viewParams)
def showFile(path, viewParams):
DataView(path, viewParams).show()
def createDataView(self, filename, viewParams={}):
return DataView(filename, viewParams)
