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 == 'doShowEigenImages':
view = DataView(self.protocol._getFileName('eigenimages'))
elif param == 'doShowReconsImages':
view = DataView(self.protocol._getFileName('reconstituted'))
elif param == 'doShowPcaFile':
view = self.textView([self.protocol.imcFile.filename.get()], "PCA file")
return [view]
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 xmipp
fn = xmipp.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewer 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, **kwargs):
labels = 'class1.id class1._representative._filename class2.id class2._representative._filename jaccard intersection union'
return [DataView(obj.outputConsensus.getFileName(),
viewParams={'order': labels, 'mode': 'metadata',
'visible': labels,
'render': 'class1._representative._filename class2._representative._filename'
})
]
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 _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 _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 _visualize(self, obj, **args):
if isinstance(obj, PcaFile):
self._views.append(self.textView([obj.getFileName()], "PCA file"))
elif isinstance(obj, SpiderProtCustomMask):
mask = obj.outputMask
self._visualize(mask)
# Visualize the whole stack with all filenames
self._views.append(DataView(mask.getFileName()))
else:
XmippViewer._visualize(self, obj)
return self._views
def visualize(self, obj, **args):
data = self.protocol._getPath('emxData/data.mrc')
DataView(data).show()
def getFileActions(self, objFile):
from pyworkflow.em.viewer import DataView
fn = objFile.getPath()
return [('Open with Xmipp viewer', lambda: DataView(fn).show(),
Icon.ACTION_VISUALIZE)]
def _showOriginalVolumeSlices(self, param=None):
out_cm = DataView(self.protocol.inputVolume.get().getFileName())
return [out_cm]
def _showVolumeSlices(self, param=None):
out_cm = DataView(self.protocol._getFileName(FN_RESOLMAP))
return [out_cm]
def _showVolumeSlices(self, param=None):
cm = DataView(self.protocol.resolution_Volume.getFileName())
return [cm]
def createDataView(self, filename, viewParams={}):
return DataView(filename, viewParams)
def _visualize(self, obj, **args):
self._views.append(ChimeraView(obj.outputPdb._chimeraScript))
self._views.append(DataView(obj._getExtraPath('pseudoatoms_approximation.vol')))
def showFile(path, viewParams):
DataView(path, viewParams).show()