def run_frequency_phase_correction(population, workspace_dir, study_id,
voxel_name, svs_type):
for subject in population:
print '###################################################################'
print 'Running Frequency and phase drift Correction for subject:', subject
subject_dir = mkdir_path(os.path.join(workspace_dir, subject,
study_id))
twx_dir = os.path.join(subject_dir, 'SVS', voxel_name, 'TWIX')
# Run frequency and phase drift correction
os.chdir(twx_dir)
if svs_type == 'PRESS':
preproc = [
'matlab', '-nodesktop', '-nosplash', '-noFigureWindows',
'-r "run_pressproc_auto(\'%s\') ; quit;"' % voxel_name
]
fpd_name = '%s_lcm' % voxel_name
elif svs_type == 'MEGA_PRESS':
preproc = [
'matlab', '-nodesktop', '-nosplash', '-noFigureWindows',
'-r "run_megapressproc_auto(\'%s\') ; quit;"' % voxel_name
]
fpd_name = '%s_diff_lcm' % voxel_name
if not os.path.isfile(os.path.join(twx_dir, voxel_name, fpd_name)):
subprocess.call(preproc)
def init_data():
# list数据保存路径
# 日志保存路径
utils.mkdir_path(DATA_LIST_PATH)
utils.mkdir_path(LOG_PATH)
# 日志配置
log_name = LOG_PATH + "/get_data_list.log"
utils.logConfig(log_name)
#数据获取总量初始化
#用于程序中断后重新启动，其初始页码应该等于当前已经获取最大页码数+1
startIndex = utils.get_curr_max_pageno(DATA_LIST_PATH) + 1
endIndex = total_page_count + 1
for x in range(startIndex, endIndex):
temp_queue.put(x)
info = "加入队列总页数：" + str(temp_queue.qsize())
logging.info(info)
print(info)
def make_svs_anatomical(population, workspace, voxel_name):
for subject in population:
subject_dir = os.path.join(workspace, subject)
dicom_dir = os.path.join(subject_dir, 'DICOM')
svs_dir = os.path.join(subject_dir, 'SVS')
nifti_dir = mkdir_path(os.path.join(subject_dir, 'NIFTI'))
########## Get MP2RAGE UNI
if not os.path.isfile( os.path.join(nifti_dir, 'ANATOMICAL.nii')):
print 'Converting MP2RAGE '
dicoms = [os.path.join(dicom_dir, dicom) for dicom in os.listdir(dicom_dir)]
T1_list = []
for dicom in dicoms:
try:
dcm_read = pydicom.read_file(dicom, force=True)
sequence = dcm_read.SeriesDescription
except AttributeError:
continue
if 'mp2rage_p3_602B_UNI_Images' in sequence:
T1_list.append(dicom)
# convert T1 anatomical to NIFTI with SPM
print 'Converting Dicom to Nifti for %s' % subject
spm_dicom_convert = spmu.DicomImport()
spm_dicom_convert.inputs.format = 'nii'
spm_dicom_convert.inputs.in_files = T1_list
spm_dicom_convert.inputs.output_dir = nifti_dir
spm_dicom_convert.run()
# rename output file
os.system('mv %s/*nii %s/ANATOMICAL.nii' %(nifti_dir, nifti_dir))
# make svs mask
rda =[]
if not os.path.isfile(os.path.join(svs_dir, voxel_name, 'RDA', '.nii')):
for root, dirs, files, in os.walk(os.path.join(svs_dir, voxel_name, 'RDA'), topdown=False):
for name in files:
if 'supp' in name and 'edit1' in name:
rda.append(os.path.join(name))
if rda is []:
print 'RDA metabolite data does not exist for subject %s' % subject
T1Path = os.path.join(subject_dir, 'NIFTI' + '/')
T1Image = 'ANATOMICAL.nii'
svs_path = os.path.join(svs_dir, voxel_name, 'RDA' + '/')
svs_file = rda[0]
matlab_command = ['matlab', '--version', '8.2', '-nodesktop', '-nosplash', '-nojvm',
'-r "RDA_TO_NIFTI(\'%s\', \'%s\', \'%s\', \'%s\') ; quit;"'
% (T1Path, T1Image, svs_path, svs_file)]
subprocess.call(matlab_command)
os.system('mv %s/*Mask.nii %s' % (nifti_dir, os.path.join(svs_dir, voxel_name, 'RDA')))
os.system('mv %s/*coord.txt %s' % (nifti_dir, os.path.join(svs_dir, voxel_name, 'RDA')))
def make_report(population, workspace, voxel_name):
for subject in population:
subdir = os.path.join(workspace_dir, subject)
rdadir = os.path.join(subdir, 'SVS', voxel_name, 'RDA')
twxdir = os.path.join(subdir, 'SVS', voxel_name, 'TWIX')
lcmdir = mkdir_path(os.path.join(twxdir, 'lcmodel'))
rda = []
for root, dirs, files, in os.walk(rdadir, topdown=False):
for name in files:
if 'supp' in name and 'edit1' in name:
rda.append(os.path.join(rdadir, name))
reader = open(rda[0], 'r')
for line in reader:
if 'SeriesDescription' in line:
Series = line[19:30]
elif 'TR:' in line:
TR = line[4:8]
elif 'TE:' in line:
TE = line[4:6]
elif 'VectorSize' in line:
nfil = line[12:16]
elif 'NumberOfAverages' in line:
NS = line[18:21]
elif 'PatientSex' in line:
Sex = line[12:13]
elif 'PatientAge' in line: #
Age = line[13:15]
elif 'PixelSpacingRow' in line:
PSR = float(line[17:19])
elif 'PixelSpacingCol' in line:
PSC = float(line[17:20])
elif 'PixelSpacing3D:' in line:
PS3d = float(line[16:19])
elif 'StudyDate' in line:
datex = line[0:19]
lcm_plot = os.path.join(twxdir, '%s_lcmodel-0.png' % voxel_name[0:3])
if not os.path.isfile(lcm_plot):
lcmodel = os.path.join(twxdir, 'lcmodel', 'ps.pdf')
make_png = ['convert', '-density', '300', '-trim', '%s' % lcmodel,# '-quality', '300', '-sharpen', '0x1.0',
'%s/%s_lcmodel.png' % (twxdir,voxel_name[0:3])]
subprocess.call(make_png)
#make report
anat = os.path.join(subdir, 'NIFTI', 'ANATOMICAL.nii')
svs = os.path.join(subdir, 'SVS', voxel_name, 'RDA/RDA_Mask.nii')
# get data into matrix
anat_load = nb.load(anat)
svs_load = nb.load(svs)
anat_data = anat_load.get_data()
svs_data = svs_load.get_data()
# get svs cut coords
coords = np.round(find_cut_coords(svs_load))
print coords
# convert zeros to nans for visualization purposes
svs_data[svs_data == 0] = np.nan
# plot voxel on anat
fig = plt.figure()
fig.set_size_inches(6.5, 6.5)
fig.subplots_adjust(wspace=0.005)
# 1
ax1 = plt.subplot2grid((1, 3), (0, 0), colspan=1, rowspan=1)
ax1.imshow(anat_data[int(coords[0]), :, :], matplotlib.cm.bone_r)
ax1.imshow(svs_data[int(coords[0]), :, :], matplotlib.cm.rainbow_r, alpha=0.7)
ax1.set_xlim(23, 157)
ax1.set_ylim(101, 230)
ax1.axes.get_yaxis().set_visible(False)
ax1.axes.get_xaxis().set_visible(False)
# 2
ax2 = plt.subplot2grid((1, 3), (0, 1), colspan=1, rowspan=1)
ax2.imshow(np.rot90(anat_data[:, :, int(coords[2])]), matplotlib.cm.bone_r)
ax2.imshow(np.rot90(svs_data[:, :, int(coords[2])]), matplotlib.cm.rainbow_r, alpha=0.7)
ax2.set_xlim(230, 20)
ax2.set_ylim(207, 4)
ax2.axes.get_yaxis().set_visible(False)
ax2.axes.get_xaxis().set_visible(False)
# 3
ax3 = plt.subplot2grid((1, 3), (0, 2), colspan=1, rowspan=1)
ax3.imshow(anat_data[:, int(coords[1]), :], matplotlib.cm.bone_r, origin='lower')
ax3.imshow(svs_data[:, int(coords[1]), :], matplotlib.cm.rainbow_r, alpha=0.7, origin='lower')
ax3.set_xlim(38, 140)
ax3.set_ylim(160, 60)
ax3.axes.get_yaxis().set_visible(False)
ax3.axes.get_xaxis().set_visible(False)
fig.tight_layout()
fig.savefig('%s/localization_%s.png' % (twxdir, voxel_name), dpi=200, bbox_inches='tight')
# create qc report
report = canvas.Canvas(os.path.join(twxdir, 'QC_REPORT_%s.pdf' % voxel_name), pagesize=(1280, 1556))
report.setFont("Helvetica", 40)
report.drawImage(os.path.join(twxdir, 'localization_%s.png' % voxel_name), 1, inch * 13.5)
report.drawImage(lcm_plot, 30, inch * 1, width=1200, height=800, mask='auto')
report.setFont("Helvetica", 30)
report.drawString(175, inch * 20, ' %s (%s-%s), TR=%s, TE=%s, NAV=%s ,Volume=%sx%sx%s'
% (subject, Age, Sex, TR, TE, NS, int(PSR), int(PSC), int(PS3d)))
# report.showPage()
report.save()
def lcmodel_gaba(population, workspace, voxel_name, water = True):
for subject in population:
twxdir = os.path.join(workspace_dir, subject, 'SVS', voxel_name, 'TWIX')
lcmdir = mkdir_path(os.path.join(twxdir, 'lcmodel'))
metdir = mkdir_path(os.path.join(twxdir, 'lcmodel', 'met'))
h2odir = mkdir_path(os.path.join(twxdir, 'lcmodel', 'h2o'))
shutil.copy(os.path.join(twxdir, voxel_name, '%s_diff_lcm'%voxel_name), os.path.join(metdir, 'RAW'))
met = os.path.join(metdir, 'RAW')
if water:
shutil.copy(os.path.join(twxdir, '%s_w'%voxel_name , '%s_w_lcm'%voxel_name), os.path.join(h2odir, 'RAW'))
h2o = os.path.join(h2odir, 'RAW')
dow = 'T'
else:
dow = 'F'
hdr = [line.rstrip('\n') for line in open(os.path.join(twxdir, voxel_name, '%s_diff_lcm'%voxel_name), 'r')][0:12]
print hdr
print ''
echot = [hdr[hdr.index(item)] for item in hdr if 'echot' in item ][0][8:]
hzpppm = [hdr[hdr.index(item)] for item in hdr if 'hzpppm' in item ][0][9:]
nunfil = [hdr[hdr.index(item)] for item in hdr if 'NumberOfPoints' in item ][0][17:]
deltat = [hdr[hdr.index(item)] for item in hdr if 'dwellTime=' in item ][0][12:]
ppmst = 4.2
ppmend = 1.95
file = open(os.path.join(lcmdir, 'control'), "w")
file.write(" $LCMODL\n")
file.write(" title= 'TWIX - %s' \n" %voxel_name)
file.write(" srcraw= '%s' \n" % met)
if water:
file.write(" srch2o= '%s' \n" % h2o)
file.write(" savdir= '%s' \n" % lcmdir)
file.write(" ppmst= %s \n"%ppmst )
file.write(" ppmend= %s\n"%ppmend)
file.write(" nunfil= %s\n" % nunfil)
file.write(" ltable= 7\n")
file.write(" lps= 8\n")
file.write(" lprint= 6\n")
file.write(" lcsv= 11\n")
file.write(" lcoraw= 10\n")
file.write(" lcoord= 9\n")
file.write(" hzpppm= %s\n" % hzpppm)
file.write(" filtab= '%s/table'\n" % lcmdir)
file.write(" filraw= '%s/met/RAW'\n" % lcmdir)
file.write(" filps= '%s/ps'\n" % lcmdir)
file.write(" filpri= '%s/print'\n" % lcmdir)
file.write(" filh2o= '%s/h2o/RAW'\n" % lcmdir)
file.write(" filcsv= '%s/spreadsheet.csv'\n" % lcmdir)
file.write(" filcor= '%s/coraw'\n" % lcmdir)
file.write(" filcoo= '%s/coord'\n" % lcmdir)
file.write(" filbas= '/home/raid3/kanaan/.lcmodel/basis-sets/mega-press-3t-1.basis'\n")
file.write(" echot= %s \n" % echot)
file.write(" dows= %s \n" %dow)
file.write(" NEACH= 999 \n") # export met fits
file.write(" doecc= T\n")
file.write(" deltat= %s\n" % deltat)
file.write(" sptype= mega-press-3")
file.write(" $END\n")
file.close()
lcm_command = ['/bin/sh', '/home/raid3/kanaan/.lcmodel/execution-scripts/standardA4pdfv3', '%s' % lcmdir, '30', '%s' % lcmdir, '%s' % lcmdir]
print subprocess.list2cmdline(lcm_command)
subprocess.call(lcm_command)
def run_frequency_phase_correction(population, workspace_dir, study_id, voxel_name, svs_type):
for subject in population:
subject_dir = os.path.join(workspace_dir, subject, study_id)
twx_dir = os.path.join(subject_dir, 'SVS', voxel_name, 'TWIX')
lcm_dir = mkdir_path(os.path.join(subject_dir, 'LCMODEL', voxel_name, 'TWIX'))
met_dir = mkdir_path(os.path.join(lcm_dir, 'met'))
h2o_dir = mkdir_path(os.path.join(lcm_dir, 'h2o'))
def make_press_control_file(lcmodel_dir, met, h2o, title, ppmst, ppmend):
hdr = [line.rstrip('\n') for line in open(met, 'r')][0:12]
print hdr
echot = [hdr[hdr.index(item)] for item in hdr if 'echot' in item][0][8:]
hzpppm = [hdr[hdr.index(item)] for item in hdr if 'hzpppm' in item][0][9:]
nunfil = [hdr[hdr.index(item)] for item in hdr if 'NumberOfPoints' in item][0][17:]
deltat = [hdr[hdr.index(item)] for item in hdr if 'dwellTime=' in item][0][12:]
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
Building the control file
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
print '...building control file'
file = open(os.path.join(lcmodel_dir, 'control'), "w")
file.write(" $LCMODL\n")
file.write(" title= 'TWIX - %s' \n" % title)
file.write(" srcraw= '%s' \n" % met)
file.write(" srch2o= '%s' \n" % h2o)
file.write(" savdir= '%s' \n" % lcmodel_dir)
file.write(" ppmst= %s \n" % ppmst)
file.write(" ppmend= 0.3\n")
file.write(" nunfil= %s\n" % nunfil)
file.write(" ltable= 7\n")
file.write(" lps= 8\n")
file.write(" lprint= 6\n")
file.write(" lcsv= 11\n")
file.write(" lcoraw= 10\n")
file.write(" lcoord= 9\n")
file.write(" hzpppm= %s\n" % hzpppm)
file.write(" filtab= '%s/table'\n" % lcmodel_dir)
file.write(" filraw= '%s/met/RAW'\n" % lcmodel_dir)
file.write(" filps= '%s/ps'\n" % lcmodel_dir)
file.write(" filpri= '%s/print'\n" % lcmodel_dir)
file.write(" filh2o= '%s/h2o/RAW'\n" % lcmodel_dir)
file.write(" filcsv= '%s/spreadsheet.csv'\n" % lcmodel_dir)
file.write(" filcor= '%s/coraw'\n" % lcmodel_dir)
file.write(" filcoo= '%s/coord'\n" % lcmodel_dir)
file.write(" filbas= '/home/raid3/kanaan/.lcmodel/basis-sets/press_te30_3t_01a.basis'\n")
file.write(" echot= %s \n" % echot)
file.write(" dows= T \n")
# file.write(" NEACH= 999 \n") # export met fits
# file.write(" DEGPPM =0 \n")
file.write(" doecc= T\n")
file.write(" deltat= %s\n" % deltat)
file.write(" $END\n")
file.close()
lcm_command = ['/bin/sh', '/home/raid3/kanaan/.lcmodel/execution-scripts/standardA4pdfv3', '%s' % lcmodel_dir,
'30', '%s' % lcmodel_dir, '%s' % lcmodel_dir]
print subprocess.list2cmdline(lcm_command)
subprocess.call(lcm_command)
def make_megapress_control_file(lcmodel_dir, met, h2o, title, ppmst, ppmend):
hdr = [line.rstrip('\n') for line in open(met, 'r')][0:12]
print hdr
echot = [hdr[hdr.index(item)] for item in hdr if 'echot' in item][0][8:]
hzpppm = [hdr[hdr.index(item)] for item in hdr if 'hzpppm' in item][0][9:]
nunfil = [hdr[hdr.index(item)] for item in hdr if 'NumberOfPoints' in item][0][17:]
deltat = [hdr[hdr.index(item)] for item in hdr if 'dwellTime=' in item][0][12:]
file = open(os.path.join(lcmodel_dir, 'control'), "w")
file.write(" $LCMODL\n")
file.write(" title= 'TWIX - %s' \n" % voxel_name)
file.write(" srcraw= '%s' \n" % met)
file.write(" srch2o= '%s' \n" % h2o)
file.write(" savdir= '%s' \n" % lcmodel_dir)
file.write(" ppmst= %s \n" % ppmst)
file.write(" ppmend= %s\n" % ppmend)
file.write(" nunfil= %s\n" % nunfil)
file.write(" ltable= 7\n")
file.write(" lps= 8\n")
file.write(" lprint= 6\n")
file.write(" lcsv= 11\n")
file.write(" lcoraw= 10\n")
file.write(" lcoord= 9\n")
file.write(" hzpppm= %s\n" % hzpppm)
file.write(" filtab= '%s/table'\n" % lcmodel_dir)
file.write(" filraw= '%s/met/RAW'\n" % lcmodel_dir)
file.write(" filps= '%s/ps'\n" % lcmodel_dir)
file.write(" filpri= '%s/print'\n" % lcmodel_dir)
file.write(" filh2o= '%s/h2o/RAW'\n" % lcmodel_dir)
file.write(" filcsv= '%s/spreadsheet.csv'\n" % lcmodel_dir)
file.write(" filcor= '%s/coraw'\n" % lcmodel_dir)
file.write(" filcoo= '%s/coord'\n" % lcmodel_dir)
file.write(" filbas= '/home/raid3/kanaan/.lcmodel/basis-sets/mega-press-3t-1.basis'\n")
file.write(" echot= %s \n" % echot)
file.write(" dows= T \n")
#file.write(" NEACH= 999 \n") # export met fits
file.write(" doecc= T\n")
file.write(" deltat= %s\n" % deltat)
file.write(" sptype= mega-press-3")
file.write(" $END\n")
file.close()
lcm_command = ['/bin/sh', '/home/raid3/kanaan/.lcmodel/execution-scripts/standardA4pdfv3', '%s' % lcmodel_dir,
'30', '%s' % lcmodel_dir, '%s' % lcmodel_dir]
print subprocess.list2cmdline(lcm_command)
subprocess.call(lcm_command)
if svs_type == 'PRESS':
if not os.path.join(lcm_dir, 'ps.pdf'):
shutil.copy(os.path.join(twx_dir, voxel_name, '%s_lcm' % voxel_name), os.path.join(met_dir, 'RAW'))
shutil.copy(os.path.join(twx_dir, '%s_w' % voxel_name, '%s_w_lcm' % voxel_name), os.path.join(h2o_dir, 'RAW'))
met = os.path.join(met_dir, 'RAW')
h2o = os.path.join(h2o_dir, 'RAW')
make_press_control_file(lcm_dir, met, h2o, '%s - %s' % (subject, voxel_name), 4.0, 0)
elif svs_type == 'MEGA_PRESS':
if not os.path.join(lcm_dir, 'ps.pdf'):
shutil.copy(os.path.join(twx_dir, voxel_name, '%s_diff_lcm' % voxel_name), os.path.join(met_dir, 'RAW'))
shutil.copy(os.path.join(twx_dir, '%s_w' % voxel_name, '%s_w_lcm' % voxel_name), os.path.join(h2o_dir, 'RAW'))
met = os.path.join(met_dir, 'RAW')
h2o = os.path.join(h2o_dir, 'RAW')
def check_spectra(population, workspace_dir, afs_dir, study_day, voxel_name,
sequence):
for subject in population:
print '####################################################'
# Input/outut dirs
subject_afs = os.path.join(afs_dir, subject, study_day)
subject_dir = mkdir_path(
os.path.join(workspace_dir, subject, study_day))
if sequence is 'PRESS':
seq = 'se'
elif sequence is 'MEGA_PRESS':
seq = 'mp'
##COPY TWIX
twx_met_src = glob.glob(
os.path.join(subject_afs, 'SVS', voxel_name, 'TWIX', voxel_name,
'*'))[0]
twx_h2o_src = glob.glob(
os.path.join(subject_afs, 'SVS', voxel_name, 'TWIX',
'%s_w' % voxel_name, '*'))[0]
twx_met_out = mkdir_path(
os.path.join(subject_dir, 'SVS', voxel_name, 'TWIX', voxel_name))
twx_h2o_out = mkdir_path(
os.path.join(subject_dir, 'SVS', voxel_name, 'TWIX',
'%s_w' % voxel_name))
if not os.listdir(twx_met_out):
print 'Copying TWIX data for Subject %s voxel %s' % (subject,
voxel_name)
os.system('cp %s %s/%s.dat' %
(twx_met_src, twx_met_out, voxel_name))
os.system('cp %s %s/%s_w.dat ' %
(twx_h2o_src, twx_h2o_out, voxel_name))
else:
print 'TWIX data for Subject %s voxel %s already copied' % (
subject, voxel_name)
#COPY RDA
if sequence is 'MEGA_PRESS':
vox = voxel_name[:-1]
else:
vox = voxel_name
rda_met_src = os.path.join(subject_afs, 'SVS', voxel_name, 'RDA',
'%s%s.rda' % (seq, vox))
rda_h2o_src = os.path.join(subject_afs, 'SVS', voxel_name, 'RDA',
'%s%sref.rda' % (seq, vox))
rda_met_out = mkdir_path(
os.path.join(subject_dir, 'SVS', voxel_name, 'RDA', voxel_name))
rda_h2o_out = mkdir_path(
os.path.join(subject_dir, 'SVS', voxel_name, 'RDA',
'%s_w' % voxel_name))
if not os.listdir(rda_met_out):
print 'Copying RDA data for Subject %s voxel %s' % (subject,
voxel_name)
os.system('cp %s %s/%s.rda' %
(rda_met_src, rda_met_out, voxel_name))
os.system('cp %s %s/%s_w.rda' %
(rda_h2o_src, rda_h2o_out, voxel_name))
else:
print 'RDA data for Subject %s voxel %s already copied' % (
subject, voxel_name)