def createRunscripts(filename, jobFile):
"""
createRunscripts:
"""
from pytom.tools.files import dump2TextFile, getPytomPath
text = '#!/bin/bash\n'
text += 'pytom ' + getPytomPath() + '/bin/mcoEXMX.py -j ' + jobFile + '\n'
dump2TextFile(filename, text, append=False)
def createRunscripts(filename,parameters):
"""
createRunscripts:
"""
from pytom.tools.files import dump2TextFile,getPytomPath
text = '#!/bin/bash\n'
text += 'pytom ' + getPytomPath() + '/bin/reconstructWB.py ' + parameters
dump2TextFile(filename, text,append = False)
def dumpMsg2Log(self,logfile,msg):
"""
dumpMsg2Log:
@param logfile:
@param msg:
@author: Thomas Hrabe
"""
from pytom.tools.files import dump2TextFile
dump2TextFile(logfile,msg)
def createRunscripts(filename, jobFile, x, y, z):
"""
createRunscripts:
"""
from pytom.tools.files import dump2TextFile, getPytomPath
text = '#!/bin/bash\n'
text += 'pytom ' + getPytomPath(
) + '/bin/localization.py ' + jobFile + ' %d %d %d' % (x, y, z) + '\n'
dump2TextFile(filename, text, append=False)
def showRotations(self,volume,directory,mask=None):
"""
showRotations: Will store x,y,z slice through volume after each rotation was applied
"""
from pytom.tools.toImage import volumeToPNG
from pytom.tools.files import dump2TextFile
from pytom_volume import vol,rotateSpline
from pytom.tools.files import getPytomPath,readStringFile
from pytom.frontend.htmlDefines import headResponse200,copyright
pytomPath = getPytomPath()
cssDefines = readStringFile(pytomPath + '/frontend/htmlDefines/CSS.css')
html = '<html>' + cssDefines
html = html + '\n<title>PyTom Alignment</title>\n'
html = html + '<body><center><h1 type="Main">List of Rotations</h1></center>\n'
html = html + '</br></br></br></br></br></br></br></br><center>\n'
html = html + '<table>\n'
html = html + '<tr><td>Z1 (Phi) Z2 (Psi) X(Theta)</td><td>x-Slice</td><td>y-Slice</td><td>z-Slice</td></tr>'
rotated = vol(volume.sizeX(),volume.sizeY(),volume.sizeZ())
if not mask:
mask = vol(volume.sizeX(),volume.sizeY(),volume.sizeZ())
mask.setAll(1)
volume = volume * mask
self.reset()
rotation = self.nextRotation()
rotationCounter = 0
while not rotation == [None,None,None]:
rotateSpline(volume,rotated,rotation[0],rotation[1],rotation[2])
html = html + '<tr><td>' + str(rotation[0]) + ' ' + str(rotation[1]) + ' ' + str(rotation[2]) +'</td>/n'
volumeToPNG(rotated,directory + str(rotationCounter) + '-x.png',rotated.sizeX()/2,'x')
html = html + '<td><img src="' + directory + str(rotationCounter) + '-x.png"/></td>'
volumeToPNG(rotated,directory + str(rotationCounter) + '-y.png',rotated.sizeY()/2,'y')
html = html + '<td><img src="' + directory + str(rotationCounter) + '-y.png"/></td>'
volumeToPNG(rotated,directory + str(rotationCounter) + '-z.png',rotated.sizeZ()/2,'z')
html = html + '<td><img src="' + directory + str(rotationCounter) + '-z.png"/></td>'
rotation = self.nextRotation()
rotationCounter = rotationCounter + 1
html = html + '</body></html>'
dump2TextFile(directory + 'rotations.html',html)
def setUp(self):
from pytom.tools.files import dump2TextFile
#from pytom_mpi import rank
#exeNames = ['openmpirun','mpirun']
#runMPI = [exeNames[i] for i in range(len(exeNames)) if self.is_exe(exeNames[i])]
runMPI = 'mpirun'
print(runMPI)
self.testCommand = runMPI + ' -c 2 pytom testScript.py'
testScript = 'from pytom_mpi import rank,init,isInitialised,finalise \n'
testScript += 'import os\n'
testScript += 'init()\n'
testScript += 'os.system("echo " +str(rank())+ " > " +str(rank())+ ".rnkPyTom" )\n'
testScript += 'finalise()\n'
dump2TextFile('testScript.py',testScript)