def _showOriginalVolumeSlices(self, param=None):
"""
This function opens the two half maps to visualize the slices
"""
cm = DataView(self.protocol.half1.get().getFileName())
cm2 = DataView(self.protocol.half2.get().getFileName())
return [cm, cm2]
def _viewLevelFiles(self, e=None):
views = []
errors = []
levelFiles = glob.glob(self.protocol._getExtraPath("results_classes_level*.xmd"))
if levelFiles:
levelFiles.sort()
lastLevelFile = levelFiles[-1]
if self.doShowLastLevel:
views.append(DataView("classes@" + lastLevelFile))
else:
if self.showSeveralLevels.empty():
self.formWindow.showError('Please select the levels that you want to visualize.')
else:
listOfLevels = []
try:
listOfLevels = self._getListFromRangeString(self.showSeveralLevels.get())
except Exception:
errors.append('Invalid levels range.')
# lastLevel = int(re.search('level_(\d\d)',lastLevelFile).group(1))
# if max(listOfLevels) <= lastLevel:
for level in listOfLevels:
fn = self.protocol._getExtraPath("results_classes_level_%02d.xmd" % level)
if os.path.exists(fn):
views.append(DataView("classes@" + fn))
else:
self.formWindow.showError('Level %s does not exist.' % level)
self.errorList(errors, views)
return views
def _showOriginalVolumeSlices(self, param=None):
if self.protocol.hasAttribute('halfVolumes'):
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):
view = 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 _showOriginalVolumeSlices(self, param=None):
# if self.protocol.halfVolumes.get() is True:
# Where is halfVolumes?
try:
cm = DataView(self.protocol.inputVolume.get().getFileName())
cm2 = DataView(self.protocol.inputVolume2.get().getFileName())
return [cm, cm2]
except:
cm = DataView(self.protocol.inputVolumes.get().getFileName())
return [cm]
def _showOriginalVolumeSlices(self, param=None):
if self.protocol.useHalfVolumes.get():
if self.protocol.hasHalfVolumesFile.get():
fn1, fn2 = self.protocol.associatedHalves.get().getHalfMaps().split(',')
else:
fn1 = self.protocol.halfMap1.get().getFileName()
fn2 = self.protocol.halfMap2.get().getFileName()
cm = DataView(fn1)
cm2 = DataView(fn2)
return [cm, cm2]
else:
cm = DataView(self.protocol.fullMap.get().getFileName())
return [cm]
def _viewParam(self, param=None):
view = 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 _viewVolume(self, e=None):
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, **args):
data = self.protocol._getPath('emxData/data.mrc')
DataView(data).show()
# open EMX file in web browser
fn = self.protocol._getPath('emxData/data.emx')
text._open_cmd(fn, self.getTkRoot())
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 _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 _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 os.path.exists(plotFn):
views.append(DataView(plotFn))
else:
showError("File not found",
"Contour plot file not found: %s" % plotFn,
self.getTkRoot())
return views
def _visualize(self, obj, **args):
import os
fnVolume = self.protocol._getExtraPath("volumeAvg.mrc")
if os.path.exists(fnVolume):
fnDir = self.protocol._getExtraPath()
samplingRate = self.protocol.readInfoField(fnDir, "sampling",
emlib.MDL_SAMPLINGRATE)
self._views.append(
ObjectView(self._project,
None,
fnVolume,
viewParams={
showj.RENDER: 'image',
showj.SAMPLINGRATE: samplingRate
}))
fnSwarm = self.protocol._getExtraPath("swarm.xmd")
if os.path.exists(fnSwarm):
self._views.append(
DataView('bestByVolume@' + fnSwarm,
viewParams={showj.MODE: showj.MODE_MD}))
return self._views
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.PYTHON, pw.getViewerScript(), 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):
from pwem import emlib
fn = emlib.FileName(path)
if fn is not None and (fn.isImage() or fn.isMetaData()):
# fn is None if xmippLib is the xmippLib ghost library
from pwem.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 _showVolumeShowj(self):
return [DataView(self._getVolumeName())]
def createDataView(self, filename, viewParams={}):
return DataView(filename, viewParams)
def _showVolumeSlices(self, param=None):
cm = DataView(self.protocol.resolution_Volume.getFileName())
return [cm]
def _showDoASlices(self, param=None):
cm = DataView(self.protocol._getExtraPath(OUTPUT_DOA_FILE))
return [cm]
def _showVolumeSlices(self, param=None):
out_cm = DataView(self.protocol._getFileName(FN_RESOLMAP))
return [out_cm]
def _showDirectionalFilter(self, param=None):
"""
The directionally filtered map using the 3DFSC as low pass filter
"""
cm = DataView(self.protocol._getExtraPath(OUTPUT_DIRECTIONAL_FILTER))
return [cm]
def _show3DFSC(self, param=None):
"""
This function opens the slices of the 3DFSC
"""
cm = DataView(self.protocol._getExtraPath(OUTPUT_3DFSC))
return [cm]
def _viewInfo(self, fn):
""" Display the info block in the metadata for a level convergence. """
return DataView('info@' + fn)
def showFile(path, viewParams):
DataView(path, viewParams).show()
def _showOriginalVolumeSlices(self, param=None):
cm = DataView(self.protocol.volumeHalf1.get().getFileName())
cm2 = DataView(self.protocol.volumeHalf2.get().getFileName())
return [cm, cm2]
def _showVolumeSlices(self, param=None):
cm = DataView(self.protocol._getFileName(RESMAP_VOL))
return [cm]
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 createDataView(self, filename, viewParams={}):
return DataView(filename, env=self._env, viewParams=viewParams)
