def show(self, form, *params):
prot = form.protocol
acquisitionInfo = prot.loadAcquisitionInfo()
if prot.importFilePath:
if exists(prot.importFilePath):
if acquisitionInfo:
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg,
form.root)
if response:
for k, v in acquisitionInfo.iteritems():
form.setVar(k, v)
else:
dialog.showWarning("Import failed",
"Could not import acquisition info.",
form.root)
else:
dialog.showError(
"Input error", "*Import file doesn't exist.*\nFile:\n%s" %
prot.importFilePath, form.root)
else:
dialog.showError("Input error", "Select import file first",
form.root)
def launchBoxingGUIStep(self):
# Print the eman version, useful to report bugs
self.runJob(eman2.Plugin.getProgram('e2version.py'), '')
useNewBoxer = self._useNewBoxer()
# Program to execute and it arguments
boxerVersion = 'old' if not useNewBoxer else 'new'
boxer = eman2.Plugin.getBoxerCommand(boxerVersion=boxerVersion)
program = eman2.Plugin.getProgram(boxer)
arguments = "%(inputMics)s"
if useNewBoxer:
arguments += " --apix=%(pixSize)f --boxsize=%(boxSize)d"
arguments += " --ptclsize=%(ptclSize)d --gui --threads=%(thr)d --no_ctf"
self._params.update({
'pixSize': self.inputMics.getSamplingRate(),
'boxSize': self.boxSize.get(),
'ptclSize': self.particleSize.get(),
'thr': self.numberOfThreads.get()
})
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' +
arguments % self._params)
self.runJob(program, arguments % self._params)
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT,
None):
self.check_gauss()
self._leaveDir() # going back to project dir
self._createOutput(self.getWorkingDir())
def deleteProject(self, projName):
if askYesNo(
Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT,
self.root):
self.manager.deleteProject(projName)
self.createProjectList(self.text)
def launchBoxingGUIStep(self):
# Print the eman version, useful to report bugs
self.runJob(Plugin.getProgram('e2version.py'), '')
# Program to execute and it arguments
program = Plugin.getProgram('e2boxer.py')
arguments = " --apix=%(pixSize)f --boxsize=%(boxSize)d"
arguments += " --ptclsize=%(ptclSize)d --gui --threads=%(thr)d --no_ctf"
self._params.update({
'pixSize': self.inputMics.getSamplingRate(),
'boxSize': self.boxSize.get(),
'ptclSize': self.particleSize.get(),
'thr': self.numberOfThreads.get()
})
arguments += " --device=%s" % self.device.get()
arguments += " %(inputMics)s"
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' +
arguments % self._params)
self.runJob(program, arguments % self._params, cwd=self.getCoordsDir())
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT,
None):
self._createOutput(self.getCoordsDir())
def launchBoxingGUIStep(self):
self.info_path = self._getExtraPath('info')
lastOutput = None
if self.getOutputsSize() >= 1:
pwutils.makePath(self.info_path)
self.json_files, self.tomo_files = jsonFilesFromSet(self.inputTomograms.get(), self.info_path)
lastOutput = [output for _, output in self.iterOutputAttributes()][-1]
_ = setCoords3D2Jsons(self.json_files, lastOutput)
if lastOutput is not None:
volIds = lastOutput.aggregate(["MAX", "COUNT"], "_volId", ["_volId"])
volIds = dict([(d['_volId'], d["COUNT"]) for d in volIds])
else:
volIds = dict()
tomoList = []
for tomo in self.inputTomograms.get().iterItems():
tomogram = tomo.clone()
if tomo.getObjId() in volIds:
tomogram.count = volIds[tomo.getObjId()]
else:
tomogram.count = 0
tomoList.append(tomogram)
tomoProvider = TomogramsTreeProvider(tomoList, self.info_path, "json")
self.dlg = EmanDialog(None, self._getExtraPath(), provider=tomoProvider,)
# Open dialog to request confirmation to create output
import tkinter as tk
frame = tk.Frame()
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, frame):
self._createOutput()
def _showEmanCtf(self, paramName=None):
program = eman2.Plugin.getProgram('e2ctf.py')
args = '--allparticles --minptcl=0 --minqual=0'
args += ' --gui --constbfactor=-1.0 --sf=auto'
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob(program,
args,
cwd=self.protocol._getExtraPath(),
numberOfMpi=1,
numberOfThreads=1)
# Open dialog to request confirmation to overwrite output
saveChanges = askYesNo(
"Save output changes?",
"Do you want to overwrite output particles with new CTF values?\n"
"This may take a while depending on the set size.",
self.getTkRoot())
if saveChanges:
self.protocol.createOutputStep()
showInfo("Output updated",
"Output particles were updated with new CTF values.",
self.getTkRoot())
def _deleteLabel(self, e=None):
selection = self.tree.getSelectedObjects()
if selection:
labelsStr = '\n'.join('- %s' % l.getName() for l in selection)
if dialog.askYesNo(
"Delete a label", "Are you sure to delete the "
"following label(s)?\n %s" % labelsStr, self):
for label in selection:
self.labels.deleteLabel(label)
self.tree.update()
def _deleteLabel(self, e=None):
selection = self.tree.getSelectedObjects()
if selection:
labelsStr = '\n'.join('- %s' % l.getName() for l in selection)
if dialog.askYesNo("Delete a label",
"Are you sure to delete the "
"following label(s)?\n %s" % labelsStr, self):
for label in selection:
self.labels.deleteLabel(label)
self.tree.update()
def deleteProject(self, projInfo):
projName = projInfo.projName
if askYesNo(
Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT,
self.root):
self.manager.deleteProject(projName)
#Delete the frame
self.text.children[self._PROJ_CONTAINER].children[
projInfo.index].grid_forget()
def _visualize(self, obj, **kwargs):
views = []
cls = type(obj)
if issubclass(cls, tomo.objects.SetOfCoordinates3D):
outputCoords = obj
tomos = outputCoords.getPrecedents()
volIds = outputCoords.aggregate(["MAX", "COUNT"], "_volId",
["_volId"])
volIds = [(d['_volId'], d["COUNT"]) for d in volIds]
tomoList = []
for objId in volIds:
tomogram = tomos[objId[0]].clone()
tomogram.count = objId[1]
tomoList.append(tomogram)
path = self.protocol._getExtraPath()
info_path = self.protocol._getExtraPath('info')
tomoProvider = TomogramsTreeProvider(
tomoList,
info_path,
'json',
)
if not os.path.exists(info_path):
pwutils.makePath(info_path)
json_files, _ = jsonFilesFromSet(tomos, info_path)
_ = setCoords3D2Jsons(json_files, outputCoords)
setView = EmanDialog(self._tkRoot, path, provider=tomoProvider)
import tkinter as tk
frame = tk.Frame()
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT,
frame):
jsons2SetCoords3D(self.protocol, outputCoords.getPrecedents(),
info_path)
elif issubclass(cls, ProtImportCoordinates3D):
if obj.getOutputsSize() >= 1:
for _, out in obj.iterOutputAttributes(
tomo.objects.SetOfCoordinates3D):
lastOutput = out
self._visualize(lastOutput)
return views
def launchBoxingGUIStep(self):
# Print the eman version, useful to report bugs
self.runJob(eman2.getEmanProgram('e2version.py'), '')
# Program to execute and it arguments
program = eman2.getEmanProgram("e2boxer.py")
arguments = "%(inputMics)s"
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + arguments % self._params)
self.runJob(program, arguments % self._params)
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, None):
self.check_gauss()
self._leaveDir()# going back to project dir
self._createOutput(self.getWorkingDir())
def launchBoxingGUIStep(self):
# First we go to runs directory (we create if it does not exist)
#path.makePath("runs")
# Program to execute and it arguments
program = eman2.getEmanProgram("e2boxer.py")
arguments = "%(inputMics)s"
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + arguments % self._params)
self.runJob(program, arguments % self._params)
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, None):
self.check_gauss()
self._leaveDir()# going back to project dir
self._createOutput(self.getWorkingDir())
def interactiveSelStep(self):
selection_file = self._getExtraPath('selected_ids.txt')
metadata = self._getExtraPath(self.CLASSES_MD)
self.classes = self.inputClasses.get()
self.mdOut = md.MetaData(metadata)
if self.intSel.get():
img_paths = np.unique(
np.asarray([
rep.getFileName()
for rep in self.classes.iterRepresentatives()
]))
pos = self.mdOut.getColumnValues(md.MDL_DIMRED)
img_ids = self.mdOut.getColumnValues(md.MDL_REF)
occupancy = self.mdOut.getColumnValues(md.MDL_CLASS_COUNT)
occupancy = np.asarray(occupancy)
pos = np.vstack(pos)
# Read selected ids from previous runs (if they exist)
if os.path.isfile(selection_file):
self.selection = np.loadtxt(selection_file)
self.selection = [int(self.selection)] if self.selection.size == 1 else \
self.selection.astype(int).tolist()
else:
self.selection = None
view = ScatterImageMarker(pos=pos,
img_paths=img_paths,
ids=img_ids,
occupancy=occupancy,
prevsel=self.selection)
view.initializePlot()
self.selection = view.selected_ids
# Save selected ids for interactive mode
np.savetxt(selection_file, np.asarray(self.selection))
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT,
None):
self._createOutputStep()
else:
self.selection = [
self.mdOut.getValue(md.MDL_REF, row.getObjId())
for row in md.iterRows(self.mdOut)
]
self._createOutputStep()
def launchParticlePickGUIStep(self):
# Launch the particle picking GUI
outputdir = self._getExtraPath()
for mic in self.inputMics:
micfile = abspath(mic.getFileName())
args = "%s %s" % (micfile, outputdir)
self.runJob("ln -sf", args)
self._enterDir(outputdir)
bsoft.loadEnvironment()
for mic in self.inputMics:
self.runJob("bshow", basename(mic.getFileName()))
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT,
None):
self._leaveDir() # going back to project dir
self._createOutput(outputdir)
def launchParticlePickGUIStep(self):
# Launch the particle picking GUI
outputdir = self._getExtraPath()
for mic in self.inputMics:
micfile = abspath(mic.getFileName())
args = "%s %s"%(micfile, outputdir)
self.runJob("ln -sf", args)
self._enterDir(outputdir)
bsoft.loadEnvironment()
for mic in self.inputMics:
self.runJob("bshow", basename(mic.getFileName()))
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, None):
self._leaveDir()# going back to project dir
self._createOutput(outputdir)
def show(self, form, *params):
prot = form.protocol
acquisitionInfo = prot.loadAcquisitionInfo()
if prot.importFilePath:
if exists(prot.importFilePath):
if acquisitionInfo:
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg, form.root)
if response:
for k, v in acquisitionInfo.iteritems():
form.setVar(k, v)
else:
dialog.showWarning("Import failed",
"Could not import acquisition info.", form.root)
else:
dialog.showError("Input error", "*Import file doesn't exist.*\nFile:\n%s" % prot.importFilePath, form.root)
else:
dialog.showError("Input error", "Select import file first", form.root)
def _setAcquisition(cls, form, acquisitionInfo):
""" Ask whether to set the AcquisitionInfo to the protocol parameters.
Params:
acquisitionInfo: Should be a dictionary with acquisition values.
If None, show an error.
"""
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition", msg, form.root)
if response:
prot = form.protocol
comment = ''
for k, v in acquisitionInfo.iteritems():
if prot.hasAttribute(k):
form.setVar(k, v)
else:
comment += "%s = %s\n" % (k, v)
if comment:
prot.setObjComment(comment)
def _setAcquisition(self, form, acquisitionInfo):
""" Ask whether to set the AcquisitionInfo to the protocol parameters.
Params:
acquisitionInfo: Should be a dictionary with acquisition values.
If None, show an error.
"""
msg = ''
for k, v in acquisitionInfo.iteritems():
msg += '%s = %s\n' % (k, v)
msg += '\n*Do you want to use detected acquisition values?*'
response = dialog.askYesNo("Import acquisition",
msg, form.root)
if response:
prot = form.protocol
comment = ''
for k, v in acquisitionInfo.iteritems():
if prot.hasAttribute(k):
form.setVar(k, v)
else:
comment += "%s = %s\n" % (k, v)
if comment:
prot.setObjComment(comment)
def deleteProject(self, projName):
if askYesNo(Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT, self.root):
self.manager.deleteProject(projName)
self.createProjectList(self.text)