def createImagicBatchFileScaling(self):
# IMAGIC batch file creation
filename = os.path.join(self.params['rundir'], "prepareStack.batch")
f = open(filename, 'w')
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
append_log = False ### log file for imagic MRA, appended only if options are given
#### Bin down stack, low-pass filter and high-pass filter images
if self.params['bin'] > 1:
f.write(
str(self.imagicroot) +
"/stand/coarse.e <<EOF > prepareStack.log\n")
f.write("start\n")
f.write("start_coarse\n")
f.write(str(self.params['bin']) + "\n")
f.write("EOF\n")
f.write(
str(self.imagicroot) +
"/stand/im_rename.e <<EOF >> prepareStack.log\n")
f.write("start_coarse\n")
f.write("start\n")
f.write("EOF\n")
append_log = True
if self.params['highpass'] is not None and self.params[
'lowpass'] is not None:
### convert to IMAGIC-specific filtering parameters
highpass, lowpass = apIMAGIC.convertFilteringParameters(
self.params['highpass'], self.params['lowpass'],
self.params['apix'])
f.write(
str(self.imagicroot) + "/incore/incband.e OPT BAND-PASS <<EOF")
if append_log is True:
f.write(" >> prepareStack.log\n")
else:
f.write(" > prepareStack.log\n")
f.write("start\n")
f.write("start_filt\n")
f.write(str(highpass) + "\n")
f.write("0\n")
f.write(str(lowpass) + "\n")
f.write("NO\n")
f.write("EOF\n")
f.write(
str(self.imagicroot) +
"/stand/im_rename.e <<EOF >> prepareStack.log\n")
f.write("start_filt\n")
f.write("start\n")
f.write("EOF\n")
append_log = True
f.close()
return filename
def createImagicBatchFileScaling(self):
# IMAGIC batch file creation
filename = os.path.join(self.params["rundir"], "prepareStack.batch")
f = open(filename, "w")
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
append_log = False ### log file for imagic MRA, appended only if options are given
#### Bin down stack, low-pass filter and high-pass filter images
if self.params["bin"] > 1:
f.write(str(self.imagicroot) + "/stand/coarse.e <<EOF > prepareStack.log\n")
f.write("start\n")
f.write("start_coarse\n")
f.write(str(self.params["bin"]) + "\n")
f.write("EOF\n")
f.write(str(self.imagicroot) + "/stand/im_rename.e <<EOF >> prepareStack.log\n")
f.write("start_coarse\n")
f.write("start\n")
f.write("EOF\n")
append_log = True
if self.params["highpass"] is not None and self.params["lowpass"] is not None:
### convert to IMAGIC-specific filtering parameters
highpass, lowpass = apIMAGIC.convertFilteringParameters(
self.params["highpass"], self.params["lowpass"], self.params["apix"]
)
f.write(str(self.imagicroot) + "/incore/incband.e OPT BAND-PASS <<EOF")
if append_log is True:
f.write(" >> prepareStack.log\n")
else:
f.write(" > prepareStack.log\n")
f.write("start\n")
f.write("start_filt\n")
f.write(str(highpass) + "\n")
f.write("0\n")
f.write(str(lowpass) + "\n")
f.write("NO\n")
f.write("EOF\n")
f.write(str(self.imagicroot) + "/stand/im_rename.e <<EOF >> prepareStack.log\n")
f.write("start_filt\n")
f.write("start\n")
f.write("EOF\n")
append_log = True
f.close()
return filename
def createImagicBatchFileMRA(self):
# IMAGIC batch file creation
##### DELETE HEADERS!!!!!!!!!!
apIMAGIC.copyFile(self.params['rundir'], "start.hed", headers=True)
apIMAGIC.copyFile(self.params['rundir'],
"references.hed",
headers=True)
filename = os.path.join(self.params['rundir'], "imagicMRA.batch")
f = open(filename, 'w')
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
append_log = False ### log file for imagic MRA, appended only if options are given
#### OPTION OF PREPARING MULTI-REFERENCE ALIGNMENT REFERENCES
if (self.params['refs'] is True
and self.params['thresh_refs'] is not None
and self.params['maskrad_refs'] is not None):
f.write(str(self.imagicroot) + "/align/alirefs.e <<EOF")
if append_log is True:
f.write(" >> multiReferenceAlignment.log\n")
else:
f.write(" > multiReferenceAlignment.log\n")
f.write("ALL\n")
f.write("CCF\n")
f.write("references\n")
f.write("NO\n")
f.write(str(self.params['maskrad_refs']) + "\n")
f.write("references_prep\n")
f.write(str(self.params['thresh_refs']) + "\n")
f.write("0.1\n")
f.write("-180,180\n")
if self.params['mirror'] is True:
f.write("YES\n")
f.write("NO\n")
f.write("TANDEM\n")
else:
f.write("NO\n")
f.write("5\n")
f.write("NO\n")
f.write("EOF\n")
f.write(
str(self.imagicroot) +
"/stand/im_rename.e <<EOF >> multiReferenceAlignment.log\n")
f.write("references_prep\n")
f.write("references\n")
f.write("EOF\n")
append_log = True
### if centering is specified, center particle in a reference-free translational alignment to the total sum
if self.params['center'] is True:
if self.params['nproc'] > 1:
f.write(str(self.imagicroot)+"/openmpi/bin/mpirun -np "+str(self.params['nproc'])+\
" -x IMAGIC_BATCH "+str(self.imagicroot)+"/align/alimass.e_mpi <<EOF")
if append_log is True:
f.write(" >> multiReferenceAlignment.log\n")
else:
f.write(" > multiReferenceAlignment.log\n")
f.write("YES\n")
f.write(str(self.params['nproc']) + "\n")
else:
f.write(str(self.imagicroot) + "/align/alimass.e <<EOF")
if append_log is True:
f.write(" >> multiReferenceAlignment.log\n")
else:
f.write(" > multiReferenceAlignment.log\n")
f.write("NO\n")
f.write("start\n")
f.write("start_cent\n")
f.write("TOTSUM\n")
f.write("CCF\n")
f.write(str(self.params['max_shift_orig']) + "\n")
f.write("3\n")
f.write("NO_FILTER\n")
f.write("EOF\n")
# f.write(str(self.imagicroot)+"/stand/im_rename.e <<EOF >> multiReferenceAlignment.log\n")
# f.write("start_cent\n")
# f.write("start\n")
# f.write("EOF\n")
append_log = True
### multi-reference alignment
if self.params['nproc'] > 1:
f.write(str(self.imagicroot)+"/openmpi/bin/mpirun -np "+str(self.params['nproc'])+\
" -x IMAGIC_BATCH "+str(self.imagicroot)+"/align/mralign.e_mpi <<EOF")
### there is a bug in IMAGIC that makes the logfile tremendously big
# if append_log is True:
# f.write(" >> multiReferenceAlignment.log\n")
# else:
# f.write(" > multiReferenceAlignment.log\n")
f.write("\n")
f.write("YES\n")
f.write(str(self.params['nproc']) + "\n")
else:
f.write(str(self.imagicroot) + "/align/mralign.e <<EOF")
### there is a bug in IMAGIC that makes the logfile tremendously big
# if append_log is True:
# f.write(" >> multiReferenceAlignment.log\n")
# else:
# f.write(" > multiReferenceAlignment.log\n")
f.write("\n")
f.write("NO\n")
f.write("FRESH\n")
f.write("ALL_REFERENCES\n")
f.write("ALIGNMENT\n")
f.write("%s\n" % (self.params['alignment_type']))
if self.params['alignment_type'].lower() == "all":
f.write("%s\n" % (self.params['first_alignment']))
if self.params['alignment_type'].lower() == "brute_force":
f.write("%d\n" % (self.params['num_orientations']))
f.write("CCF\n")
if self.params['center'] is True:
f.write("start_cent\n")
else:
f.write("start\n")
f.write("alignstack\n")
f.write("start\n")
f.write("references\n")
if self.params['lowpass_refs'] is not None:
hpfilt_imagic, lpfilt_imagic = apIMAGIC.convertFilteringParameters(
"", self.params['lowpass_refs'], self.params['apix'])
f.write("LOWPASS\n")
f.write(str(lpfilt_imagic) + "\n")
else:
f.write("NO\n")
f.write("NO\n")
f.write(str(self.params['max_shift_orig']) + "\n")
if self.params['center'] is True:
f.write(str(self.params['max_shift_this']) + "\n")
f.write("-180,180\n")
if self.params['center'] is True:
f.write("-180,180\n")
f.write("INTERACTIVE\n")
f.write(str(self.params['samp_param']) + "\n")
f.write(
str(self.params['minrad']) + "," + str(self.params['maxrad']) +
"\n")
f.write(str(self.params['numiter']) + "\n")
f.write("NO\n")
f.write("EOF\n")
### write out alignment parameters to file
f.write(
str(self.imagicroot) +
"/stand/headers.e <<EOF >> multiReferenceAlignment.log\n")
f.write("PLT\n")
f.write("INDEX\n")
f.write("NUMBER_OF_INDEX\n")
f.write("100;112;113;104;107\n"
) ### rotation, shiftx, shifty, ccc, reference num
# f.write("NO\n")
f.write("alignstack\n")
f.write("outparams.plt\n")
f.write("EOF\n")
f.close()
return filename
def createImagicBatchFileMRA(self):
# IMAGIC batch file creation
##### DELETE HEADERS!!!!!!!!!!
apIMAGIC.copyFile(self.params['rundir'], "start.hed", headers=True)
apIMAGIC.copyFile(self.params['rundir'], "references.hed", headers=True)
filename = os.path.join(self.params['rundir'], "imagicMRA.batch")
f = open(filename, 'w')
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
append_log = False ### log file for imagic MRA, appended only if options are given
#### OPTION OF PREPARING MULTI-REFERENCE ALIGNMENT REFERENCES
if (self.params['refs'] is True and self.params['thresh_refs'] is not None and self.params['maskrad_refs'] is not None):
f.write(str(self.imagicroot)+"/align/alirefs.e <<EOF")
if append_log is True:
f.write(" >> multiReferenceAlignment.log\n")
else:
f.write(" > multiReferenceAlignment.log\n")
f.write("ALL\n")
f.write("CCF\n")
f.write("references\n")
f.write("NO\n")
f.write(str(self.params['maskrad_refs'])+"\n")
f.write("references_prep\n")
f.write(str(self.params['thresh_refs'])+"\n")
f.write("0.1\n")
f.write("-180,180\n")
if self.params['mirror'] is True:
f.write("YES\n")
f.write("NO\n")
f.write("TANDEM\n")
else:
f.write("NO\n")
f.write("5\n")
f.write("NO\n")
f.write("EOF\n")
f.write(str(self.imagicroot)+"/stand/im_rename.e <<EOF >> multiReferenceAlignment.log\n")
f.write("references_prep\n")
f.write("references\n")
f.write("EOF\n")
append_log = True
### if centering is specified, center particle in a reference-free translational alignment to the total sum
if self.params['center'] is True:
if self.params['nproc'] > 1:
f.write(str(self.imagicroot)+"/openmpi/bin/mpirun -np "+str(self.params['nproc'])+\
" -x IMAGIC_BATCH "+str(self.imagicroot)+"/align/alimass.e_mpi <<EOF")
if append_log is True:
f.write(" >> multiReferenceAlignment.log\n")
else:
f.write(" > multiReferenceAlignment.log\n")
f.write("YES\n")
f.write(str(self.params['nproc'])+"\n")
else:
f.write(str(self.imagicroot)+"/align/alimass.e <<EOF")
if append_log is True:
f.write(" >> multiReferenceAlignment.log\n")
else:
f.write(" > multiReferenceAlignment.log\n")
f.write("NO\n")
f.write("start\n")
f.write("start_cent\n")
f.write("TOTSUM\n")
f.write("CCF\n")
f.write(str(self.params['max_shift_orig'])+"\n")
f.write("3\n")
f.write("NO_FILTER\n")
f.write("EOF\n")
# f.write(str(self.imagicroot)+"/stand/im_rename.e <<EOF >> multiReferenceAlignment.log\n")
# f.write("start_cent\n")
# f.write("start\n")
# f.write("EOF\n")
append_log = True
### multi-reference alignment
if self.params['nproc'] > 1:
f.write(str(self.imagicroot)+"/openmpi/bin/mpirun -np "+str(self.params['nproc'])+\
" -x IMAGIC_BATCH "+str(self.imagicroot)+"/align/mralign.e_mpi <<EOF")
### there is a bug in IMAGIC that makes the logfile tremendously big
# if append_log is True:
# f.write(" >> multiReferenceAlignment.log\n")
# else:
# f.write(" > multiReferenceAlignment.log\n")
f.write("\n")
f.write("YES\n")
f.write(str(self.params['nproc'])+"\n")
else:
f.write(str(self.imagicroot)+"/align/mralign.e <<EOF")
### there is a bug in IMAGIC that makes the logfile tremendously big
# if append_log is True:
# f.write(" >> multiReferenceAlignment.log\n")
# else:
# f.write(" > multiReferenceAlignment.log\n")
f.write("\n")
f.write("NO\n")
f.write("FRESH\n")
f.write("ALL_REFERENCES\n")
f.write("ALIGNMENT\n")
f.write("%s\n" % (self.params['alignment_type']))
if self.params['alignment_type'].lower() == "all":
f.write("%s\n" % (self.params['first_alignment']))
if self.params['alignment_type'].lower() == "brute_force":
f.write("%d\n" % (self.params['num_orientations']))
f.write("CCF\n")
if self.params['center'] is True:
f.write("start_cent\n")
else:
f.write("start\n")
f.write("alignstack\n")
f.write("start\n")
f.write("references\n")
if self.params['lowpass_refs'] is not None:
hpfilt_imagic, lpfilt_imagic = apIMAGIC.convertFilteringParameters("", self.params['lowpass_refs'], self.params['apix'])
f.write("LOWPASS\n")
f.write(str(lpfilt_imagic)+"\n")
else:
f.write("NO\n")
f.write("NO\n")
f.write(str(self.params['max_shift_orig'])+"\n")
if self.params['center'] is True:
f.write(str(self.params['max_shift_this'])+"\n")
f.write("-180,180\n")
if self.params['center'] is True:
f.write("-180,180\n")
f.write("INTERACTIVE\n")
f.write(str(self.params['samp_param'])+"\n")
f.write(str(self.params['minrad'])+","+str(self.params['maxrad'])+"\n")
f.write(str(self.params['numiter'])+"\n")
f.write("NO\n")
f.write("EOF\n")
### write out alignment parameters to file
f.write(str(self.imagicroot)+"/stand/headers.e <<EOF >> multiReferenceAlignment.log\n")
f.write("PLT\n")
f.write("INDEX\n")
f.write("NUMBER_OF_INDEX\n")
f.write("100;112;113;104;107\n") ### rotation, shiftx, shifty, ccc, reference num
# f.write("NO\n")
f.write("alignstack\n")
f.write("outparams.plt\n")
f.write("EOF\n")
f.close()
return filename
