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normalisation_comparison.py
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normalisation_comparison.py
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# normalisation_comparison | "Normalises" a number of 3D brain images
# by applying factors based on the median signal intensity calculated at
# the previous step.
# an internal reference) to a brain atlas.
# Please see the user manual for details.
#
# Copyright (C) 2015, Dimitri Perrin
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from time import localtime, strftime
from subprocess import call
import ast
import sys
if len(sys.argv)!=2:
print "\nUsage: "+sys.argv[0]+" <parameter_file>"
quit()
# Reading the parameters
parameter_file = open(sys.argv[1],'r')
parameters = []
for line in parameter_file:
if line[0] == "#":
continue
parameters.append(line.rstrip())
parameter_file.close()
# Processing the parameters
merged_dir = parameters[0]
brains = parameters[1].split(",")
internal_ref = parameters[2]
temp = parameters[3].split(",")
median = dict()
for i in range(0,len(brains)):
median[brains[i]] = ast.literal_eval(temp[i])
neg_brain = parameters[4]
pos_brain = parameters[5]
log = parameters[6]
# Checking the parameters
print "The method will: "
print " - read/write NIfTI-1 from/to "+merged_dir
print "\nBrains to be processed: "
print brains
print "\nInternal reference brain: "
print internal_ref
print "\nMedian intensity: "
print median
print "\nNegative (control) brain: "
print neg_brain
print "\nPositive brain: "
print pos_brain
print " "
while 1:
feedback = raw_input("Is this correct? (yes/no)\t").rstrip()
if feedback == "yes":
print "Program starting...\n"
break
if feedback == "no":
print "Please edit the parameter file."
quit()
# Running the analysis step
log_file = open(log,'w')
# calculating the highest value
highestMedian = 0
for el in median:
val = median[el]
if val > highestMedian:
highestMedian = val
# Normalisation
output_message = strftime("%H:%M:%S", localtime())+": Normalising."
print output_message
log_file.write(output_message+"\n")
for i in range(0,len(brains)):
normalisationFactor = highestMedian/median[brains[i]]
raw = merged_dir+brains[i]+"_geneExp_aligned_"+internal_ref+".nii.gz"
normd = merged_dir+brains[i]+"_geneExp_aligned_"+internal_ref+"_normalised.nii.gz"
if brains[i]==internal_ref:
raw = merged_dir+brains[i]+"_geneExp.nii.gz"
normd = merged_dir+brains[i]+"_geneExp_normalised.nii.gz"
cmd = "fslmaths "+raw+" -mul "+str(normalisationFactor)+" "+normd
call([cmd],shell=True)
# Difference between two brains
output_message = strftime("%H:%M:%S", localtime())+": Subtracting brains."
print output_message
log_file.write(output_message+"\n")
neg = merged_dir+neg_brain+"_geneExp_aligned_"+internal_ref+"_normalised.nii.gz"
if neg_brain == internal_ref:
neg = merged_dir+neg_brain+"_geneExp_normalised.nii.gz"
pos = merged_dir+pos_brain+"_geneExp_aligned_"+internal_ref+"_normalised.nii.gz"
if pos_brain == internal_ref:
pos = merged_dir+pos_brain+"_geneExp_normalised.nii.gz"
diff = merged_dir+"sub_"+neg_brain+"_from_"+pos_brain+"_normalised.nii.gz"
cmd = "fslmaths "+pos+" -sub "+neg+" "+diff
call([cmd],shell=True)
output_message = strftime("%H:%M:%S", localtime())+": Done."
print output_message
log_file.write(output_message+"\n")
log_file.close()