def toHTMLFile(self,filename):
"""
toHTMLFile: Overrides parent method and stores CorrelationMatrixJob to HMTL
@param filename: HTML filename
"""
from lxml import etree
import io
from pytom.tools.files import getPytomPath,readStringFile
pytomPath = getPytomPath()
xsltString = readStringFile(pytomPath + '/xslt/CorrelationMatrix.xsl')
xsltStringIO = io.StringIO(xsltString)
selfHTML = self.xsltTransform(xsltStringIO)
htmlString = etree.tostring(selfHTML,pretty_print=True)
file = open(filename, "w")
file.write(htmlString)
file.close()
def readRotationsFromEMFile(self, filename, inputIsInRadians=True):
"""
readRotationsFromEMFile: Reads rotations from EM file and optionally converts them from radians to degrees
@param filename: Name of EM file
@param inputIsInRadians:
@type inputIsInRadians: bool
"""
self._angleList = []
if not filename == '':
import pytom_volume
from pytom.angles.angle import rad2deg
try:
angs = pytom_volume.read(filename)
except RuntimeError:
from pytom.tools.files import checkFileExists, getPytomPath
if not checkFileExists(filename):
filename = getPytomPath(
) + '/angles/angleLists/' + filename
angs = pytom_volume.read(filename)
for i in range(angs.sizeY()):
phi = angs.getV(0, i, 0)
psi = angs.getV(1, i, 0)
the = angs.getV(2, i, 0)
if inputIsInRadians:
phi = phi * rad2deg
psi = psi * rad2deg
the = the * rad2deg
self._angleList.append([phi, psi, the])
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 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 run(parameters, verbose=True):
"""
run: Determines Path / URL to documentation files
"""
from pytom.tools.files import getPytomPath
pytomPath = getPytomPath()
apiDocPath = pytomPath + '/doc/index.html'
if verbose:
print('API DOC PATH : ', apiDocPath)
return apiDocPath
def __init__(self,
filename='',
inputIsInRadians=True,
refinementParameters=None):
"""
___init__:
@param filename: Filename of em file storing rotations. New files must have the naming (angles_INCREMENT_NUMBERROTATIONS.em) below. Set to either one of these:
angles_3_553680.em angles_07_45123.em angles_11_15192.em angles_12.85_7112.em angles_17.86_3040.em angles_18_3040.em angles_19.95_1944.em angles_25.25_980.em angles_35.76_320.em angles_38.53_256.em angles_50_100.em angles_90_26.em angles_inf_0.em
@param inputIsInRadians: Are the input values in radiants (True is assumed as default)
@param refinementParameters: Parameters for next refinement step
@author: Thomas Hrabe
"""
from pytom.tools.files import checkFileExists, getPytomPath
import os
if checkFileExists(filename):
self._filename = filename
else:
if os.sep in filename:
#parse angle file name out of filename
splitName = filename.split(os.sep)
filename = splitName[-1]
if not filename[-3:] == '.em':
filename = filename + '.em'
self._filename = getPytomPath() + '/angles/angleLists/' + filename
if checkFileExists(self._filename):
self.readRotationsFromEMFile(self._filename, inputIsInRadians)
self._currentIndex = 0
self._refinementParameters = refinementParameters or [
self._defaultShells, self._defaultIncrement
] #shells,increment
def run(parameters, verbose=False):
"""
run: Answers a http request depending on the provided parameters.
Parameters can be
XML=FILENAME
DIR=DIRNAME
ALIG=NAME
@param parameters:
"""
from pytom.basic.structures import ParticleList
from pytom.tools.files import checkDirExists, checkFileExists
if verbose:
print("Parsing particleList request!")
splitParameters = parameters.split('&')
if splitParameters.__class__ == list:
if verbose:
print(splitParameters)
for i in range(len(splitParameters)):
parameter = splitParameters[i]
split = parameter.split('=')
keyword = split[0]
argument = split[1]
if verbose:
print('Keyword : ', keyword)
print('Arguments : ', argument)
if keyword == 'XML':
from pytom.tools.files import readStringFile, getPytomPath
import io
from lxml import etree
if not checkFileExists(argument):
raise IOError('File not found!')
pl = ParticleList('/')
pl.fromXMLFile(argument)
xsltString = readStringFile(
getPytomPath() + '/frontend/html/xslt/ParticleList.xsl')
xsltTransform = io.StringIO(xsltString)
transformed = pl.xsltTransform(xsltTransform)
return etree.tostring(transformed, pretty_print=True)
elif keyword == 'DIR':
from pytom.tools.files import checkDirExists, getPytomPath, readStringFile
import io
from lxml import etree
if not checkDirExists(argument):
raise IOError('File not found!')
pl = ParticleList(argument)
pl.loadDirectory()
xsltString = readStringFile(
getPytomPath() + '/frontend/html/xslt/ParticleList.xsl')
xsltTransform = io.StringIO(xsltString)
transformed = pl.xsltTransform(xsltTransform)
return etree.tostring(transformed, pretty_print=True)
elif keyword == 'ALIG':
from pytom.tools.files import checkDirExists, getPytomPath, readStringFile
import io
from lxml import etree
if not checkDirExists(argument):
raise IOError('File not found!')
pl = ParticleList(argument)
pl.fromAlignmentFile(argument)
xsltString = readStringFile(
getPytomPath() + '/frontend/html/xslt/ParticleList.xsl')
xsltTransform = io.StringIO(xsltString)
transformed = pl.xsltTransform(xsltTransform)
return etree.tostring(transformed, pretty_print=True)
elif splitParameters.__class__ == str:
if verbose:
print(splitParameters)
def run(parameters, verbose=False):
"""
run: Answers a http request depending on the provided parameters.
Parameters can be
XML=FILENAME
DIR=DIRNAME
@param parameters:
"""
from pytom.reconstruction.reconstructionStructures import ProjectionList
from pytom.tools.files import checkDirExists, checkFileExists
from pytom.frontend.serverpages.serverMessages import ErrorMessage
splitParameters = parameters.split('&')
if splitParameters.__class__ == list:
if verbose:
print(splitParameters)
for i in range(len(splitParameters)):
parameter = splitParameters[i]
split = parameter.split('=')
keyword = split[0]
argument = split[1]
if verbose:
print('Keyword : ', keyword)
print('Arguments : ', argument)
if keyword == 'XML':
from pytom.tools.files import readStringFile, getPytomPath
import io
from lxml import etree
if not checkFileExists(argument):
print(ErrorMessage('File / directory not found!'))
return str(ErrorMessage('File / directory not found!'))
pl = ProjectionList()
pl.fromXMLFile(argument)
xsltString = readStringFile(
getPytomPath() + '/frontend/html/xslt/ProjectionList.xsl')
xsltTransform = io.StringIO(xsltString)
transformed = pl.xsltTransform(xsltTransform)
return etree.tostring(transformed, pretty_print=True)
elif keyword == 'DIR':
from pytom.tools.files import checkDirExists, getPytomPath, readStringFile
import io
from lxml import etree
if not checkDirExists(argument):
print(ErrorMessage('File / directory not found!'))
return str(ErrorMessage('File / directory not found!'))
pl = ProjectionList()
pl.loadDirectory(argument)
xsltString = readStringFile(
getPytomPath() + '/frontend/html/xslt/ProjectionList.xsl')
xsltTransform = io.StringIO(xsltString)
transformed = pl.xsltTransform(xsltTransform)
return etree.tostring(transformed, pretty_print=True)