def softMask(infile, outfile=None, mask=0.8, falloff=0.1):
"""
applies a soft mask to images in a stack
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outname)
else:
outname = fname+"_mask"
## output temporary file to same directory as original file
outfile = fname+"_mask"
myIm = pymagic.ImagicSession("stand/arithm.e")
myIm.toImagicQuiet("%s"%fname) # input
myIm.toImagicQuiet("%s"%outname) # output
myIm.toImagicQuiet("SOFT") # soft mask
myIm.toImagicQuiet("%.2f"%mask) # mask as a fraction
myIm.toImagicQuiet("%.2f"%falloff) # falloff as a fraction
myIm.close()
### check that it ran correctly
if not os.path.exists(outname+".hed"):
apDisplay.printError("arithm.e did not execute properly")
return None
return outname
def normalize(infile,
outfile=None,
sigma=10.0,
path=os.path.abspath('.'),
keepfiles=False):
"""
normalize images in a stack
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outfile)
else:
outname = fname + "_norm"
myIm = pymagic.ImagicSession("stand/pretreat.e")
imagicv = myIm.version()
myIm.toImagicQuiet(fname) # input
myIm.toImagicQuiet(outname) # output
myIm.toImagicQuiet("NORM_VARIANCE") # mode
myIm.toImagicQuiet("WHOLE") # mask to be used
myIm.toImagicQuiet("%.2f" % sigma) # desired sigma
myIm.toImagicQuiet("NO") # remove dust outliers
if imagicv >= 110119:
myIm.toImagicQuiet("NO")
myIm.close()
# check proper execution
if not os.path.exists(outname + ".hed"):
apDisplay.printError("normalization did not execute properly")
return outname
def normalize(infile, outfile=None, sigma=10.0, path=os.path.abspath('.'), keepfiles=False):
"""
normalize images in a stack
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outfile)
else:
outname=fname+"_norm"
myIm = pymagic.ImagicSession("stand/pretreat.e")
imagicv = myIm.version()
myIm.toImagicQuiet(fname) # input
myIm.toImagicQuiet(outname) # output
myIm.toImagicQuiet("NORM_VARIANCE") # mode
myIm.toImagicQuiet("WHOLE") # mask to be used
myIm.toImagicQuiet("%.2f"%sigma) # desired sigma
myIm.toImagicQuiet("NO") # remove dust outliers
if imagicv >= 110119:
myIm.toImagicQuiet("NO")
myIm.close()
# check proper execution
if not os.path.exists(outname+".hed"):
apDisplay.printError("normalization did not execute properly")
return outname
def alimass(infile, outfile=None, maxshift=0.2, ceniter=10, nproc=1):
"""
uses a rotationally averaged total sum to center particles
default max shift is 20% of box size
default # of centering iterations is 10
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outname)
else:
outname = fname + "_cen"
if nproc > 1:
myIm = pymagic.ImagicSession("align/alimass.e_mpi", nproc)
myIm.toImagicQuiet("YES")
myIm.toImagicQuiet(nproc)
else:
myIm = pymagic.ImagicSession("align/alimass.e")
myIm.toImagicQuiet("NO")
myIm.toImagicQuiet(fname)
myIm.toImagicQuiet(outname)
myIm.toImagicQuiet("TOTSUM")
myIm.toImagicQuiet("CCF")
myIm.toImagicQuiet("%.3f" % maxshift)
myIm.toImagicQuiet("%i" % ceniter)
myIm.toImagicQuiet("NO_FILTER")
myIm.close()
### check that it ran correctly
if not os.path.exists(outname + ".hed"):
apDisplay.printError("alimass.e did not execute properly")
return None
return outname
def softMask(infile, outfile=None, mask=0.8, falloff=0.1):
"""
applies a soft mask to images in a stack
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outname)
else:
outname = fname + "_mask"
## output temporary file to same directory as original file
outfile = fname + "_mask"
myIm = pymagic.ImagicSession("stand/arithm.e")
myIm.toImagicQuiet("%s" % fname) # input
myIm.toImagicQuiet("%s" % outname) # output
myIm.toImagicQuiet("SOFT") # soft mask
myIm.toImagicQuiet("%.2f" % mask) # mask as a fraction
myIm.toImagicQuiet("%.2f" % falloff) # falloff as a fraction
myIm.close()
### check that it ran correctly
if not os.path.exists(outname + ".hed"):
apDisplay.printError("arithm.e did not execute properly")
return None
return outname
def alimass(infile, outfile=None, maxshift=0.2, ceniter=10, nproc=1):
"""
uses a rotationally averaged total sum to center particles
default max shift is 20% of box size
default # of centering iterations is 10
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outname)
else:
outname = fname + "_cen"
if nproc > 1:
myIm = pymagic.ImagicSession("align/alimass.e_mpi", nproc)
myIm.toImagicQuiet("YES")
myIm.toImagicQuiet(nproc)
else:
myIm = pymagic.ImagicSession("align/alimass.e")
myIm.toImagicQuiet("NO")
myIm.toImagicQuiet(fname)
myIm.toImagicQuiet(outname)
myIm.toImagicQuiet("TOTSUM")
myIm.toImagicQuiet("CCF")
myIm.toImagicQuiet("%.3f" % maxshift)
myIm.toImagicQuiet("%i" % ceniter)
myIm.toImagicQuiet("NO_FILTER")
myIm.close()
### check that it ran correctly
if not os.path.exists(outname + ".hed"):
apDisplay.printError("alimass.e did not execute properly")
return None
return outname
def headersToFile(infile, outfile=None):
"""
writes out shift values to a file
"""
fname = pymagic.fileFilter(infile)
if not outfile:
outfile = "outparams.plt"
myIm = pymagic.ImagicSession("stand/headers.e")
if myIm.version() < 91120:
myIm.toImagicQuiet(fname)
myIm.toImagicQuiet("PLT")
myIm.toImagicQuiet("SHIFT")
myIm.toImagicQuiet(outfile)
myIm.toImagicQuiet("*")
else:
myIm.toImagicQuiet("PLT")
myIm.toImagicQuiet("SHIFT")
myIm.toImagicQuiet(fname)
myIm.toImagicQuiet(outfile)
myIm.close()
### check that it ran correctly
if not os.path.exists(outfile):
apDisplay.printError("headers.e did not execute properly")
return None
return outfile
def headersToFile(infile, outfile=None):
"""
writes out shift values to a file
"""
fname = pymagic.fileFilter(infile)
if not outfile:
outfile = "outparams.plt"
myIm = pymagic.ImagicSession("stand/headers.e")
if myIm.version() < 91120:
myIm.toImagicQuiet(fname)
myIm.toImagicQuiet("PLT")
myIm.toImagicQuiet("SHIFT")
myIm.toImagicQuiet(outfile)
myIm.toImagicQuiet("*")
else:
myIm.toImagicQuiet("PLT")
myIm.toImagicQuiet("SHIFT")
myIm.toImagicQuiet(fname)
myIm.toImagicQuiet(outfile)
myIm.close()
### check that it ran correctly
if not os.path.exists(outfile):
apDisplay.printError("headers.e did not execute properly")
return None
return outfile
def alirefs(infile,
outfile=None,
mask=0.99,
maxshift=0.3,
minrot=-180.0,
maxrot=180.0,
iter=5,
minrad=0.0,
maxrad=0.9):
"""
align a stack of references to each other
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outfile, exists=False)
else:
outname = fname + "_ali"
myIm = pymagic.ImagicSession("align/alirefs.e")
imagicv = myIm.version()
myIm.toImagicQuiet("ALL") # translation & rotation
if imagicv >= 101013:
myIm.toImagicQuiet("ROTATION_FIRST")
myIm.toImagicQuiet("CCF") # CCF or MCF
myIm.toImagicQuiet("%s" % fname) # input
myIm.toImagicQuiet("NO") # no contours on reference imgs
myIm.toImagicQuiet("%.2f" % mask) # mask as fraction
myIm.toImagicQuiet("%s" % outname) # output
myIm.toImagicQuiet("-999.") # density for thresholding
myIm.toImagicQuiet("%.2f" % maxshift) # max shift
myIm.toImagicQuiet("%.2f,%.2f" % (minrot, maxrot)) # min max rot angle
if imagicv >= 101013:
myIm.toImagicQuiet("MEDIUM") # Precision for rotational alignment
myIm.toImagicQuiet("%.2f,%.2f" %
(minrad, maxrad)) # min, max radius for rot align
myIm.toImagicQuiet("NO") # create mirrors
myIm.toImagicQuiet("%i" % iter) # alignment iterations
myIm.toImagicQuiet("NO") # full output of all parameters
myIm.close()
# check proper execution
if not os.path.exists(outname + ".hed"):
apDisplay.printError("alirefs.e did not execute properly")
return outname
def alirefs(infile, outfile=None, mask=0.99, maxshift=0.3, minrot=-180.0, maxrot=180.0, iter=5, minrad=0.0, maxrad=0.9):
"""
align a stack of references to each other
"""
fname = pymagic.fileFilter(infile)
if outfile:
outname = pymagic.fileFilter(outfile, exists=False)
else:
outname = fname + "_ali"
myIm = pymagic.ImagicSession("align/alirefs.e")
imagicv = myIm.version()
myIm.toImagicQuiet("ALL") # translation & rotation
if imagicv >= 101013:
myIm.toImagicQuiet("ROTATION_FIRST")
myIm.toImagicQuiet("CCF") # CCF or MCF
myIm.toImagicQuiet("%s" % fname) # input
myIm.toImagicQuiet("NO") # no contours on reference imgs
myIm.toImagicQuiet("%.2f" % mask) # mask as fraction
myIm.toImagicQuiet("%s" % outname) # output
myIm.toImagicQuiet("-999.") # density for thresholding
myIm.toImagicQuiet("%.2f" % maxshift) # max shift
myIm.toImagicQuiet("%.2f,%.2f" % (minrot, maxrot)) # min max rot angle
if imagicv >= 101013:
myIm.toImagicQuiet("MEDIUM") # Precision for rotational alignment
myIm.toImagicQuiet("%.2f,%.2f" % (minrad, maxrad)) # min, max radius for rot align
myIm.toImagicQuiet("NO") # create mirrors
myIm.toImagicQuiet("%i" % iter) # alignment iterations
myIm.toImagicQuiet("NO") # full output of all parameters
myIm.close()
# check proper execution
if not os.path.exists(outname + ".hed"):
apDisplay.printError("alirefs.e did not execute properly")
return outname
def mask2D(boxsz, mask, infile=False, maskfile="mask2Dimgfile"):
"""
creates a 2d circular mask
if infile is specified, mask is applied to stack & then mask is deleted
boxsz is the box size in pixels
mask is the size of the mask to apply as a fraction
"""
### generate a 2D mask
# f=open(batchfile,"w")
# f.write("#!/bin/csh -f\n")
# f.write("setenv IMAGIC_BATCH 1\n")
apDisplay.printMsg("creating 2D mask")
myIm = pymagic.ImagicSession("stand/testim.e")
myIm.toImagicQuiet("%s"%maskfile)
myIm.toImagicQuiet("%i,%i"%(boxsz,boxsz))
myIm.toImagicQuiet("real")
myIm.toImagicQuiet("disc")
myIm.toImagicQuiet("%.3f"%mask)
myIm.close()
if not infile:
# check proper execution
if not os.path.exists(maskfile+".hed"):
apDisplay.printError("mask generation did not execute properly")
return maskfile
### if infile is specified, apply mask to images
fname = pymagic.fileFilter(infile)
file_ma=fname+"_ma"
apDisplay.printMsg("applying 2D mask")
myIm = pymagic.ImagicSession("stand/twoimag.e")
myIm.toImagicQuiet("mul")
myIm.toImagicQuiet("%s"%fname)
myIm.toImagicQuiet("%s"%maskfile)
myIm.toImagicQuiet("%s"%file_ma)
myIm.close()
# check proper execution
if not os.path.exists(file_ma+".hed"):
apDisplay.printError("masking did not execute properly")
return file_ma
def mask2D(boxsz, mask, infile=False, maskfile="mask2Dimgfile"):
"""
creates a 2d circular mask
if infile is specified, mask is applied to stack & then mask is deleted
boxsz is the box size in pixels
mask is the size of the mask to apply as a fraction
"""
### generate a 2D mask
# f=open(batchfile,"w")
# f.write("#!/bin/csh -f\n")
# f.write("setenv IMAGIC_BATCH 1\n")
apDisplay.printMsg("creating 2D mask")
myIm = pymagic.ImagicSession("stand/testim.e")
myIm.toImagicQuiet("%s" % maskfile)
myIm.toImagicQuiet("%i,%i" % (boxsz, boxsz))
myIm.toImagicQuiet("real")
myIm.toImagicQuiet("disc")
myIm.toImagicQuiet("%.3f" % mask)
myIm.close()
if not infile:
# check proper execution
if not os.path.exists(maskfile + ".hed"):
apDisplay.printError("mask generation did not execute properly")
return maskfile
### if infile is specified, apply mask to images
fname = pymagic.fileFilter(infile)
file_ma = fname + "_ma"
apDisplay.printMsg("applying 2D mask")
myIm = pymagic.ImagicSession("stand/twoimag.e")
myIm.toImagicQuiet("mul")
myIm.toImagicQuiet("%s" % fname)
myIm.toImagicQuiet("%s" % maskfile)
myIm.toImagicQuiet("%s" % file_ma)
myIm.close()
# check proper execution
if not os.path.exists(file_ma + ".hed"):
apDisplay.printError("masking did not execute properly")
return file_ma
def takeoverHeaders(filename, numpart, boxsize):
### better workaround than copyFile ... still a workaround though
fname = pymagic.fileFilter(filename)
## output temporary file to same directory as original file
outpath = os.path.split(fname)[0]
outfile = os.path.join(outpath,"tempimg")
myIm = pymagic.ImagicSession("stand/testim.e")
myIm.toImagicQuiet("%s,1,%d" % (outfile,numpart))
myIm.toImagicQuiet("%d,%d" % (boxsize, boxsize))
myIm.toImagicQuiet("REAL")
myIm.toImagicQuiet("BLOBS")
myIm.close()
if not os.path.exists(outfile+".hed"):
apDisplay.printError("header rewrite failed")
apDisplay.printMsg("replacing '%s' with '%s'"%(fname+".hed",outfile+".hed"))
shutil.move(outfile+".hed", fname+".hed")
os.remove(outfile+".img")
def takeoverHeaders(filename, numpart, boxsize):
### better workaround than copyFile ... still a workaround though
fname = pymagic.fileFilter(filename)
## output temporary file to same directory as original file
outpath = os.path.split(fname)[0]
outfile = os.path.join(outpath, "tempimg")
myIm = pymagic.ImagicSession("stand/testim.e")
myIm.toImagicQuiet("%s,1,%d" % (outfile, numpart))
myIm.toImagicQuiet("%d,%d" % (boxsize, boxsize))
myIm.toImagicQuiet("REAL")
myIm.toImagicQuiet("BLOBS")
myIm.close()
if not os.path.exists(outfile + ".hed"):
apDisplay.printError("header rewrite failed")
apDisplay.printMsg("replacing '%s' with '%s'" %
(fname + ".hed", outfile + ".hed"))
shutil.move(outfile + ".hed", fname + ".hed")
os.remove(outfile + ".img")
def readIndexFromHeader(headerfilename, indexnum, numparts=100):
"""
returns the header values contained at the index
as an array of float values
Limited to the numparts if specified
"""
fname = pymagic.fileFilter(headerfilename)
headfile=open(fname+".hed",'rb')
# get number or particles in stack
nump = int('%d' % (os.stat(fname+".hed")[6]/1024))
if numparts > nump:
numparts = nump
# create array of values
headervals=[]
for particle in range(numparts+1):
headerbytes = headfile.read(1024)
headervals.append(numpy.fromstring(headerbytes,dtype=numpy.float32)[indexnum])
headfile.close()
return headervals
def readIndexFromHeader(headerfilename, indexnum, numparts=100):
"""
returns the header values contained at the index
as an array of float values
Limited to the numparts if specified
"""
fname = pymagic.fileFilter(headerfilename)
headfile = open(fname + ".hed", 'rb')
# get number or particles in stack
nump = int('%d' % (os.stat(fname + ".hed")[6] / 1024))
if numparts > nump:
numparts = nump
# create array of values
headervals = []
for particle in range(numparts + 1):
headerbytes = headfile.read(1024)
headervals.append(
numpy.fromstring(headerbytes, dtype=numpy.float32)[indexnum])
headfile.close()
return headervals
def mralign(alistack, origstack, refs, outfile=None, mask=0.8, imask=0, nproc=1):
"""
perform a multi-reference alignment
"""
aliname = pymagic.fileFilter(alistack)
stackname = pymagic.fileFilter(origstack)
refname = pymagic.fileFilter(refs)
if outfile:
outname = pymagic.fileFilter(outfile)
else:
outname = "mrastack"
if nproc > 1:
myIm = pymagic.ImagicSession("align/mralign.e_mpi", nproc)
myIm.toImagicQuiet("YES")
myIm.toImagicQuiet(nproc)
else:
myIm = pymagic.ImagicSession("align/mralign.e")
myIm.toImagicQuiet("NO")
## get imagic version
imagicv = myIm.version()
## rest of the params
myIm.toImagicQuiet("FRESH")
myIm.toImagicQuiet("ALL")
# 091120 or higher version 4D options:
if imagicv >= 91120:
myIm.toImagicQuiet("ALIGNMENT")
myIm.toImagicQuiet("ALL")
myIm.toImagicQuiet("ROTATION_FIRST")
myIm.toImagicQuiet("CCF")
myIm.toImagicQuiet(aliname)
myIm.toImagicQuiet(outname)
myIm.toImagicQuiet(stackname)
myIm.toImagicQuiet(refname)
myIm.toImagicQuiet("NO_FILTER")
# lower than 091120 version of imagic asks for mirrors:
if imagicv < 91120:
myIm.toImagicQuiet("NO")
myIm.toImagicQuiet("0.31")
# check if there are any rotations stored in the header
equivRots = apImagicFile.readIndexFromHeader(aliname, 116)
hasRots = False
for value in equivRots:
if value != 0:
hasRots = True
break
# don't ask Max shift (during this alignment) for first iteration:
if hasRots is True:
myIm.toImagicQuiet("0.2")
myIm.toImagicQuiet("-180,180")
# don't ask rotation (during this alignment) for first iteration:
if hasRots is True:
myIm.toImagicQuiet("-180,180")
myIm.toImagicQuiet("MEDIUM")
myIm.toImagicQuiet("%.2f,%.2f" % (imask, mask))
myIm.toImagicQuiet("2")
myIm.toImagicQuiet("NO")
myIm.close()
### check that it ran correctly
if not os.path.exists(outname + ".hed"):
apDisplay.printError("mralign.e did not execute properly")
return None
return outname
def mralign(alistack,
origstack,
refs,
outfile=None,
mask=0.8,
imask=0,
nproc=1):
"""
perform a multi-reference alignment
"""
aliname = pymagic.fileFilter(alistack)
stackname = pymagic.fileFilter(origstack)
refname = pymagic.fileFilter(refs)
if outfile:
outname = pymagic.fileFilter(outfile)
else:
outname = "mrastack"
if nproc > 1:
myIm = pymagic.ImagicSession("align/mralign.e_mpi", nproc)
myIm.toImagicQuiet("YES")
myIm.toImagicQuiet(nproc)
else:
myIm = pymagic.ImagicSession("align/mralign.e")
myIm.toImagicQuiet("NO")
## get imagic version
imagicv = myIm.version()
## rest of the params
myIm.toImagicQuiet("FRESH")
myIm.toImagicQuiet("ALL")
# 091120 or higher version 4D options:
if imagicv >= 91120:
myIm.toImagicQuiet("ALIGNMENT")
myIm.toImagicQuiet("ALL")
myIm.toImagicQuiet("ROTATION_FIRST")
myIm.toImagicQuiet("CCF")
myIm.toImagicQuiet(aliname)
myIm.toImagicQuiet(outname)
myIm.toImagicQuiet(stackname)
myIm.toImagicQuiet(refname)
myIm.toImagicQuiet("NO_FILTER")
# lower than 091120 version of imagic asks for mirrors:
if imagicv < 91120:
myIm.toImagicQuiet("NO")
myIm.toImagicQuiet("0.31")
# check if there are any rotations stored in the header
equivRots = apImagicFile.readIndexFromHeader(aliname, 116)
hasRots = False
for value in equivRots:
if value != 0:
hasRots = True
break
# don't ask Max shift (during this alignment) for first iteration:
if hasRots is True:
myIm.toImagicQuiet("0.2")
myIm.toImagicQuiet("-180,180")
# don't ask rotation (during this alignment) for first iteration:
if hasRots is True:
myIm.toImagicQuiet("-180,180")
myIm.toImagicQuiet("MEDIUM")
myIm.toImagicQuiet("%.2f,%.2f" % (imask, mask))
myIm.toImagicQuiet("2")
myIm.toImagicQuiet("NO")
myIm.close()
### check that it ran correctly
if not os.path.exists(outname + ".hed"):
apDisplay.printError("mralign.e did not execute properly")
return None
return outname