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ImageImportWindow.py
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# -*- coding: utf-8 -*-
#
# Importation of data in the database + image registration and normalization
#(c) Inserm U836 2012-2014 - Manik Bhattacharjee
#
# License GNU GPL v3
#
#
#TODO
#
# Tester et finaliser l'import depuis un PACS
#
# Verifier qu'on ne convertit pas une image déjà récupérée (surtout DICOM-> Nifti !)
#
# Améliorer le choix de l'image pre/post dans BrainVisa : afficher des aperçus avec Anatomist après l'import DICOM ?
# Ou coder en C++ un créateur d'aperçu DICOM avec la lib dcmtk, ou utiliser http://sourceforge.net/projects/qdcws/
#
#Optimisation : on peut supposer que le nombre de slices
# (SliceNumberMR) quand on ouvre un fichier permet de
# sauter les SliceNumberMR-1 suivants car ce sont les
# autres slices de la même image
#
# Onglet registration : mettre en vert les images qui ont déjà un recalage vers la T1pre, en gras l'image normalisée vers le template SPM
# FIXME La version suivante de BrainVisa (post 4.3) devrait corriger un bug dans l'insertion des items dans la base (en insérant les répertoires qui les contiennent)
# Il faudra alors virer la fonction createItemDirs que j'ai créé pour résoudre ce pb. D'autre part pour résoudre le pb pour les fichiers registration
# j'ai ajouté l'insertion des répertoires dans data/neuroDiskItems.py (fonction createParentDirectory) mais ça ne marche pas (import circulaires !)
# Donc à chaque ajout de référentiel ou de transfo, j'ai ajouté une ligne neuroHierarchy.databases.createDiskItemFromFileName A SUPPRIMER quand BrainVisa sera corrigé (après BV 4.3)
#dirItem=neuroHierarchy.databases.createDiskItemFromFileName(d, None)
# import pdb;pdb.set_trace() -> pour lancer le debugger quand on arrive sur cette ligne (sorte de breakpoint)
# ipython -q4thread locateElectrodes.py # Pour avoir ipython et Qt actifs en même temps au cours du debug
from PyQt4 import uic, QtGui, QtCore
import os, subprocess, re, pickle, shutil, tempfile, scipy.io, json, numpy
from scipy import ndimage
from brainvisa import axon, processes
from soma import aims
from soma.wip.application.api import Application
from brainvisa.data.writediskitem import ReadDiskItem, WriteDiskItem
from brainvisa.data import neuroHierarchy
#import anatomist.direct.api as anatomist
from brainvisa import anatomist
import registration
from externalprocesses import *
from dicomutilities import *
import seegprocessing, patientinfo, pathologypatientinfo
from checkSpmVersion import *
from freesurfer.brainvisaFreesurfer import *
from TimerMessageBox import *
import pdb
# Matlab code : coregister file1 to file2
def matlab_cellstr(listOfStrings):
""" Converts a list of filenames as a matlab-suitable cell table of strings and adds ',1' at the end of each string (for spm file lists) """
return "{'"+",1' '".join([str(stri) for stri in listOfStrings])+",1'}"
# SPM coregistration onto file1 ({'/home/manik/data/epilepsie/IRM-testOD/Pre/3DT1.img,1'}) of file 2 ({'/home/manik/data/epilepsie/IRM-testOD/Post/SagT2.img,1'})
#spm_coregister = "try, spm('defaults', 'FMRI');spm_jobman('initcfg');\
#matlabbatch{1}.spm.spatial.coreg.estimate.ref = %s;\
#matlabbatch{1}.spm.spatial.coreg.estimate.source = %s;\
#matlabbatch{1}.spm.spatial.coreg.estimate.other = {''};\
#matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\
#matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\
#matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\
#matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];\
#spm_jobman('run',matlabbatch); catch, disp 'AN ERROR OCCURED'; end;quit;"
# Coregister two files and saves the matrix in an ASCII file (space-separated)
spm_coregister = """try,addpath(genpath(%s));VF=spm_vol(%s);VG=spm_vol(%s);
centermatF = eye(4);
center_F = %s;
F_orient = %s;
F_orient = reshape(F_orient,4,4)';
centermatF(:,4) = F_orient*[center_F 1]';
centermatG = eye(4);
center_G = %s;
G_orient = %s;
G_orient = reshape(G_orient,4,4)';
centermatG(:,4) = G_orient*[center_G 1]';
centeredmatF = inv(centermatF)*VF.private.mat;
centeredmatG = inv(centermatG)*VG.private.mat;
VF.mat = centeredmatF;
VF.private.mat = centeredmatF;
VF.private.mat0 = centeredmatF;
VG.mat = centeredmatG;
VG.private.mat = centeredmatG;
VG.private.mat0 = centeredmatG;
x = spm_coreg(VF,VG);
matCoreg = spm_matrix(x(:)');
trm = centermatG*matCoreg*inv(centermatF);
trm = [trm(1:3,4)';trm(1:3,1:3)];
dlmwrite(%s,trm, 'delimiter',' ','precision',16); \n
catch, disp 'AN ERROR OCCURED'; end;quit;"""
# SPM coregistration onto file1 ({'/home/manik/data/epilepsie/IRM-testOD/Pre/3DT1.img,1'}) of file 2 ({'/home/manik/data/epilepsie/IRM-testOD/Post/SagT2.img,1'}) with reslicing
spm_coregisterReslice = "try,addpath(genpath(%s)); spm('defaults', 'FMRI');spm_jobman('initcfg');\
matlabbatch{1}.spm.spatial.coreg.estwrite.ref == %s;\
matlabbatch{1}.spm.spatial.coreg.estwrite.source = %s;\
matlabbatch{1}.spm.spatial.coreg.estwrite.other = {''};\
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.cost_fun = 'nmi';\
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.sep = [4 2];\
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.fwhm = [7 7];\
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.interp = 1;\
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.wrap = [0 0 0];\
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.mask = 0;\
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.prefix = 'r';\
spm_jobman('run',matlabbatch); catch, disp 'AN ERROR OCCURED'; end;quit;"
# SPM normalisation of file 1 ({'/home/manik/data/epilepsie/IRM-testOD/Pre/3DT1.img,1'}) onto template
#spm_template_t1 = "{'/home/manik/prog/implantation/matlab/spm8/templates/T1.nii,1'}"
#spm_template_t1 = "{'/matlab_prog/spm8_5236/templates/T1.nii,1'}"
#spm8_normalise = """try, addpath(genpath(%s)); spm('defaults', 'FMRI');spm_jobman('initcfg');
#matlabbatch{1}.spm.spatial.normalise.est.subj.source = %s;
#matlabbatch{1}.spm.spatial.normalise.est.subj.wtsrc = '';
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.template = %s;
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.weight = '';
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.smosrc = 8;
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.smoref = 0;
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.regtype = 'mni';
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.cutoff = 25;
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.nits = 16;
#matlabbatch{1}.spm.spatial.normalise.est.eoptions.reg = 1;
#spm_jobman('run',matlabbatch); catch, disp 'AN ERROR OCCURED'; end;quit;"""
spm8_normalise = """try, addpath(genpath(%s)); spm('defaults', 'FMRI');spm_jobman('initcfg');
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.source = %s;
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.wtsrc = '';
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.resample = %s;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.template = %s;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.weight = '';
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smosrc = 8;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smoref = 0;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.regtype = 'mni';
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.cutoff = 25;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.nits = 16;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.reg = 1;
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.preserve = 0;
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.bb = [-78 -112 -50
78 76 85];
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.vox = [1 1 1];
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.interp = 1;
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.prefix = 'w';
spm_jobman('run',matlabbatch); catch, disp 'AN ERROR OCCURED'; end;quit;"""
spm12_normalise = """try, addpath(genpath(%s)); spm('defaults', 'FMRI');spm_jobman('initcfg');
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.vol = %s;
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.resample = %s;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.biasreg = 0.0001;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.biasfwhm = 60;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.tpm = {%s};
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.affreg = 'mni';
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.fwhm = 0;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.samp = 3;
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.vox = [1 1 1];
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.interp = 4;
spm_jobman('run',matlabbatch); catch, disp 'AN ERROR OCCURED'; end;quit;"""
matlab_removeGado = """try, addpath(genpath(%s)); spm('defaults', 'FMRI');spm_jobman('initcfg');
matlabbatch{1}.spm.spatial.preproc.channel.vols = {%s};
matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {%s};
matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {%s};
matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {%s};
matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {%s};
matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {%s};
matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {%s};
matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 2;
matlabbatch{1}.spm.spatial.preproc.warp.write = [0 0];
spm_jobman('run',matlabbatch);
c1 = spm_vol(%s);
c2 = spm_vol(%s);
c3 = spm_vol(%s);
c4 = spm_vol(%s);
Yc1 = spm_read_vols(c1);
Yc2 = spm_read_vols(c2);
Yc3 = spm_read_vols(c3);
Yc4 = spm_read_vols(c4);
keepC1 = find(Yc1 ~= 0);
keepC2 = find(Yc2 ~= 0);
keepC3 = find(Yc3 ~= 0);
keepC4 = find(Yc4 ~= 0);
all_keep = unique([keepC1; keepC2]);
fullImage = spm_vol(%s);
YfullImage = spm_read_vols(fullImage);
all_remove = [1:1:size(YfullImage(:))];
all_remove(all_keep)=[];
YfullImage(all_remove)=0;
fullImage.fname=%s;
spm_write_vol(fullImage,YfullImage);
catch, disp 'AN ERROR OCCURED'; end;quit;"""
spm_inverse_y_field12 = """try,addpath(genpath(%s));spm('defaults', 'FMRI');spm_jobman('initcfg');
clear matlabbatch;
matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.def = {%s};
matlabbatch{1}.spm.util.defs.comp{1}.inv.space = {%s};
matlabbatch{1}.spm.util.defs.out{1}.savedef.ofname = %s;
matlabbatch{1}.spm.util.defs.out{1}.savedef.savedir.saveusr = {%s};
spm_jobman('run',matlabbatch);catch, disp 'AN ERROR OCCURED'; end;quit;"""
spm_MNItoScannerBased = """try,addpath(genpath(%s));spm('defaults', 'FMRI');spm_jobman('initcfg');
clear matlabbatch;
matlabbatch{1}.spm.spatial.normalise.write.subj.def = {%s};
matlabbatch{1}.spm.spatial.normalise.write.subj.resample = {%s};
matlabbatch{1}.spm.spatial.normalise.write.woptions.bb = [-150 -150 -150
150 150 150];
matlabbatch{1}.spm.spatial.normalise.write.woptions.vox = [1 1 1];
matlabbatch{1}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{1}.spm.spatial.normalise.write.woptions.prefix = 'tmpMNItoScannerBased';
matlabbatch{2}.spm.spatial.realign.write.data = {
%s
%s
};
matlabbatch{2}.spm.spatial.realign.write.roptions.which = [2 1];
matlabbatch{2}.spm.spatial.realign.write.roptions.interp = 4;
matlabbatch{2}.spm.spatial.realign.write.roptions.wrap = [0 0 0];
matlabbatch{2}.spm.spatial.realign.write.roptions.mask = 1;
matlabbatch{2}.spm.spatial.realign.write.roptions.prefix = '';
spm_jobman('run',matlabbatch);catch, disp 'AN ERROR OCCURED'; end;quit;"""
(Ui_ImageImportWindow, QDialog) = uic.loadUiType('ImageImportWindow.ui')
class ImageImportWindow (QDialog):
"""ImageImportWindow is the main dialog class of the Image Importer software"""
def __init__ (self, parent = None):
QDialog.__init__(self, parent)
#self.setWindowTitle('Image Import Window- NOT FOR MEDICAL USAGE')
self.ui = Ui_ImageImportWindow()
self.seriesUIDbyName = {}
self.studiesUIDbyName = {}
self.ui.setupUi(self)
self.currentProtocol = None
self.currentSubject = None
self.AcPc = {}
self.brainCenter = None
self.defaultAcqDate = QtCore.QDate(1900,1,1)
self.ui.acqDate.setDate(self.defaultAcqDate)
self.modas = {'t1mri':'Raw T1 MRI', 't2mri':'T2 MRI', 'ct': 'CT', 'pet': 'PET','fmri_epile':'fMRI-epile', 'statistic_data':'Statistic-Data', 'flair': 'FLAIR', 'freesurfer_atlas':'FreesurferAtlas', 'fgatir':'FGATIR', 'hippofreesurfer_atlas':'HippoFreesurferAtlas'}
## Init brainvisa to access the DB
axon.initializeProcesses()
# Allow calling brainvisa processes
from neuroProcesses import defaultContext
self.brainvisaContext = defaultContext()
# Get Transformation Manager
self.transfoManager = registration.getTransformationManager()
# Load anatomist
self.a = anatomist.Anatomist('-b')
layout = QtGui.QVBoxLayout( self.ui.windowContainer1 )
layout2 = QtGui.QHBoxLayout( )
layout3 = QtGui.QHBoxLayout( )
self.axWindow = self.a.createWindow( 'Axial' )#, no_decoration=True )
self.axWindow2 = self.a.createWindow( 'Sagittal' )#, no_decoration=True )
self.axWindow3 = self.a.createWindow( 'Axial' )#, no_decoration=True )
self.axWindow4 = self.a.createWindow( 'Sagittal' )#, no_decoration=True )
self.wins = [self.axWindow, self.axWindow2, self.axWindow3, self.axWindow4]
self.axWindow.setParent(self.ui.windowContainer1)
self.axWindow2.setParent(self.ui.windowContainer1)
self.axWindow3.setParent(self.ui.windowContainer1)
self.axWindow4.setParent(self.ui.windowContainer1)
layout2.addWidget( self.axWindow.getInternalRep() )
layout2.addWidget( self.axWindow2.getInternalRep() )
layout3.addWidget( self.axWindow3.getInternalRep() )
layout3.addWidget( self.axWindow4.getInternalRep() )
layout.addLayout(layout2)
layout.addLayout(layout3)
self.dispObj = []
self.initialize()
self.ui.dicomOutputPathEdit.setText(self.dicomOutputPath)
self.ui.niftiOutputPathEdit.setText(self.niftiOutputPath)
self.threads = []
self.waitingForThreads={}
# Init the patient informations tab
self.patientInfo = patientinfo.buildUI(self.ui.patGroupBox)
cdate = self.patientInfo['currentDate'].date()
bdate = self.patientInfo['patientBirthday'].date()
page = bdate.daysTo(cdate)/365
self.patientInfo['patientAge'].setText(str(page))
self.patientInfo['comoraucune'].stateChanged.connect(self.checkbox_comor)
self.patientInfo['patientBirthday'].dateChanged.connect(self.update_patientAge)
#self.pathologypatientInfo = pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)
# Recharge la BDD BrainVisa à chaque changement d'onglet
self.connect(self.ui.tabWidget, QtCore.SIGNAL('currentChanged(int)'), self.analyseBrainvisaDB)
self.connect(self.ui.tabWidget, QtCore.SIGNAL('currentChanged(int)'), self.setTabGuide)
# Brainvisa database tab
self.connect(self.ui.bvProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.bvSubjectCombo))
self.connect(self.ui.bvSubjectCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), self.selectBvSubject)
self.connect(self.ui.bvSubjectCombo, QtCore.SIGNAL('activated(QString)'), self.setCurrentSubject)
self.connect(self.ui.bvImageList, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem*)'), self.selectBvImage)
self.connect(self.ui.bvDeleteImageButton, QtCore.SIGNAL('clicked()'), self.deleteBvImage)
self.connect(self.ui.bvDeleteSubjectButton, QtCore.SIGNAL('clicked()'), self.deleteBvSubject)
# Add Subject tab
self.connect(self.ui.subjectSiteCombo, QtCore.SIGNAL('activated(QString)'), self.updatePatientCode)
self.connect(self.ui.subjectSiteCombo, QtCore.SIGNAL('editTextChanged(QString)'), self.updatePatientCode)
self.connect(self.ui.subjectYearSpinbox, QtCore.SIGNAL('valueChanged(int)'), self.updatePatientCode)
self.connect(self.ui.subjectPatientName, QtCore.SIGNAL('textChanged(QString)'), self.updatePatientCode)
self.connect(self.ui.subjectPatientFirstName, QtCore.SIGNAL('textChanged(QString)'), self.updatePatientCode)
self.connect(self.ui.subjectAddSubjectButton, QtCore.SIGNAL('clicked()'), self.storePatientInDB)
# DICOM tab
self.connect(self.ui.chooseDirButton, QtCore.SIGNAL('clicked()'), self.openDicomDir)
self.connect(self.ui.dirImportButton, QtCore.SIGNAL('clicked()'), self.importDataDir)
self.connect(self.ui.dicomOutputButton, QtCore.SIGNAL('clicked()'), lambda :self.selectOutput('Dicom'))
self.connect(self.ui.niftiOutputButton, QtCore.SIGNAL('clicked()'), lambda :self.selectOutput('Nifti'))
# PACS tab
self.connect(self.ui.pacsSearchButton, QtCore.SIGNAL('clicked()'), self.searchPacs)
self.connect(self.ui.dirPatientList, QtCore.SIGNAL('itemSelectionChanged()'), lambda :self.patientSelectionChanged('dir'))
self.connect(self.ui.pacsPatientList, QtCore.SIGNAL('itemSelectionChanged()'), lambda :self.patientSelectionChanged('pacs'))
self.connect(self.ui.dirStudiesList, QtCore.SIGNAL('itemSelectionChanged()'), lambda :self.studiesSelectionChanged('dir'))
self.connect(self.ui.pacsStudiesList, QtCore.SIGNAL('itemSelectionChanged()'), lambda :self.studiesSelectionChanged('pacs'))
self.connect(self.ui.chooseNiftiButton, QtCore.SIGNAL('clicked()'), self.chooseNifti)
self.connect(self.ui.pacsImportButton, QtCore.SIGNAL('clicked()'), self.downloadPacs)
# Import to BrainVisa for DICOM/NIFTI/PACS
#NIFTI
self.connect(self.ui.niftiImportButton, QtCore.SIGNAL('clicked()'), self.importNifti)
self.connect(self.ui.niftiSetBraincenterButton, QtCore.SIGNAL('clicked()'), self.setBrainCenter)
self.connect(self.ui.ImportFSoutputspushButton, QtCore.SIGNAL('clicked()'),self.importFSoutput)
#PACS
self.connect(self.ui.pacsImportBVButton, QtCore.SIGNAL('clicked()'), self.importPacs)
#DICOM
self.connect(self.ui.dirImportBVButton, QtCore.SIGNAL('clicked()'), self.importDir)
# NIFTI
self.connect(self.ui.niftiProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.niftiSubjectCombo))
self.connect(self.ui.niftiSubjectCombo, QtCore.SIGNAL('activated(QString)'), self.setCurrentSubject)
self.connect(self.ui.niftiSeqType, QtCore.SIGNAL('currentIndexChanged(QString)'),self.enable_disable_gadooption)
# Registration tab
self.connect(self.ui.regProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.regSubjectCombo))
self.connect(self.ui.regSubjectCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), self.selectRegSubject)
self.connect(self.ui.regSubjectCombo, QtCore.SIGNAL('activated(QString)'), self.setCurrentSubject)
self.connect(self.ui.regImageList, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem*)'), self.selectRegImage)
self.connect(self.ui.regImageList2, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem*)'), self.selectRegImage2)
self.connect(self.ui.registerNormalizeSubjectButton, QtCore.SIGNAL('clicked()'), self.registerNormalizeSubject)
self.connect(self.ui.segmentationHIPHOPbutton,QtCore.SIGNAL('clicked()'),self.segmentationHIPHOP)
self.connect(self.ui.FreeSurferReconAllpushButton,QtCore.SIGNAL('clicked()'),self.runFreesurferReconAll)
self.connect(self.ui.runMarsAtlasFreesurferButton,QtCore.SIGNAL('clicked()'),self.runMarsAtlasFreesurfer)
self.warningMEDIC()
def setDictValue(d, k, v,button):
d[k]=v
button.setStyleSheet("background-color: rgb(90, 255, 95);")
self.connect(self.ui.regAcButton, QtCore.SIGNAL('clicked()'), lambda:setDictValue(self.AcPc,'AC',list(self.a.linkCursorLastClickedPosition()),self.ui.regAcButton))
self.connect(self.ui.regPcButton, QtCore.SIGNAL('clicked()'), lambda:setDictValue(self.AcPc,'PC',list(self.a.linkCursorLastClickedPosition()),self.ui.regPcButton))
self.connect(self.ui.regIhButton, QtCore.SIGNAL('clicked()'), lambda:setDictValue(self.AcPc,'IH',list(self.a.linkCursorLastClickedPosition()),self.ui.regIhButton))
self.connect(self.ui.regLhButton, QtCore.SIGNAL('clicked()'), lambda:setDictValue(self.AcPc,'LH',list(self.a.linkCursorLastClickedPosition()),self.ui.regLhButton))
self.connect(self.ui.regAcPcValidateButton, QtCore.SIGNAL('clicked()'), self.validateAcPc)
# Implantation tab (surgery drawings)
self.connect(self.ui.implProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.implSubjectCombo))
self.connect(self.ui.implSubjectCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), self.selectImplSubject)
self.connect(self.ui.implSubjectCombo, QtCore.SIGNAL('activated(QString)'), self.setCurrentSubject)
self.connect(self.ui.implCoroOpenButton, QtCore.SIGNAL('clicked()'), self.openImplCoro)
self.connect(self.ui.implCoroImportButton, QtCore.SIGNAL('clicked()'), self.importImplCoro)
self.connect(self.ui.implSagOpenButton, QtCore.SIGNAL('clicked()'), self.openImplSag)
self.connect(self.ui.implSagImportButton, QtCore.SIGNAL('clicked()'), self.importImplSag)
self.connect(self.ui.implPptOpenButton, QtCore.SIGNAL('clicked()'), self.openImplPpt)
self.connect(self.ui.implPptImportButton, QtCore.SIGNAL('clicked()'), self.importImplPpt)
self.connect(self.ui.implPdfOpenButton, QtCore.SIGNAL('clicked()'), self.openImplPdf)
self.connect(self.ui.implPdfImportButton, QtCore.SIGNAL('clicked()'), self.importImplPdf)
self.connect(self.ui.implPdfOpenButton2, QtCore.SIGNAL('clicked()'), self.openImplPdf2)
self.connect(self.ui.implPdfImportButton2, QtCore.SIGNAL('clicked()'), self.importImplPdf2)
self.connect(self.ui.implElListPdfOpenButton, QtCore.SIGNAL('clicked()'), self.openImplElListPdf)
self.connect(self.ui.implElListPdfImportButton, QtCore.SIGNAL('clicked()'), self.importImplElListPdf)
# Infos patient tab
self.connect(self.ui.patProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.patSubjectCombo))
#self._pathologyinfo = lambda :pathologypatientinfo.buildUI()
self.connect(self.ui.patProtocolCombo, QtCore.SIGNAL('activated(QString)'),lambda :pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)) #lambda :pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)) self._pathologyinfo(self.ui.patpatGroupBox,self.currentProtocol)
self.connect(self.ui.patSubjectCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), self.selectPatSubject)
self.connect(self.ui.patSubjectCombo, QtCore.SIGNAL('activated(QString)'), self.setCurrentSubject)
self.connect(self.ui.patInfoValidate,QtCore.SIGNAL('clicked()'),self.ValidatePatInfo)
# Importation SEEG tab
self.connect(self.ui.seegProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.seegSubjectCombo))
self.connect(self.ui.seegSubjectCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), self.selectSeegSubject)
self.connect(self.ui.seegSubjectCombo, QtCore.SIGNAL('activated(QString)'), self.setCurrentSubject)
self.connect(self.ui.seegManipsBaseCombo, QtCore.SIGNAL('activated(QString)'), self.manipSelected)
self.connect(self.ui.chooseSeegButton, QtCore.SIGNAL('clicked()'), self.chooseSeeg)
self.connect(self.ui.seegImportButton, QtCore.SIGNAL('clicked()'), self.seegImport)
#Preference tab
self.connect(self.ui.prefSpmTemplateButton, QtCore.SIGNAL('clicked()'), self.setSpmTemplatePath)
self.connect(self.ui.prefANTsButton, QtCore.SIGNAL('clicked()'), self.setANTsPath)
self.connect(self.ui.prefSpmStandaloneButton, QtCore.SIGNAL('clicked()'), self.setSpmStandalonePath)
self.connect(self.ui.prefFreesurferButton, QtCore.SIGNAL('clicked()'), self.setFreesurferPath)
self.connect(self.ui.prefNoDBFileLocationButton, QtCore.SIGNAL('clicked()'),self.setNoDBFilePath)
self.connect(self.ui.prefANTScheckbox, QtCore.SIGNAL('clicked()'), lambda: self.setPrefCoregister('ANTS'))
self.connect(self.ui.prefSPMcheckbox, QtCore.SIGNAL('clicked()'), lambda: self.setPrefCoregister('SPM'))
self.connect(self.ui.prefAimscheckbox, QtCore.SIGNAL('clicked()'), lambda: self.setPrefCoregister('Aims'))
self.ui.radioButtonProject_4.toggled.connect(self.switchProjectButton)
self.ui.radioButtonProject_3.toggled.connect(self.switchProjectButton)
self.ui.radioButtonProject_2.toggled.connect(self.switchProjectButton)
self.ui.radioButtonProject.toggled.connect(self.switchProjectButton)
self.ui.radioButtonProject_4.toggled.connect(self.updatePatientCode)
self.ui.radioButtonProject_3.toggled.connect(self.updatePatientCode)
self.ui.radioButtonProject_2.toggled.connect(self.updatePatientCode)
self.ui.radioButtonProject.toggled.connect(self.updatePatientCode)
self.ui.SavePreferencespushButton.clicked.connect(self.savePreferences)
#self.connect(self.ui.radioButtonProject_3, QtCore.SIGNAL('clicked()'), lambda: self.switchProjectButton)
#self.connect(self.ui.radioButtonProject_2, QtCore.SIGNAL('clicked()'), lambda: self.switchProjectButton)
#self.connect(self.ui.radioButtonProject, QtCore.SIGNAL('clicked()'), lambda: self.switchProjectButton)
#self.connect(self.ui.radioButtonProject_3, QtCore.SIGNAL('clicked()'), lambda: self.updatePatientCode)
#self.connect(self.ui.radioButtonProject_2, QtCore.SIGNAL('clicked()'), lambda: self.updatePatientCode)
#self.connect(self.ui.radioButtonProject, QtCore.SIGNAL('clicked()'), lambda: self.updatePatientCode)
# Finds the available protocols in brainvisa database and fills the comboboxes
self.analyseBrainvisaDB()
self.setGuide("Choose on of the tabs to import data in the BrainVisa database")
self.enableACPCButtons(False)
# Disable work-in-progress tabs
#self.ui.tabWidget.setTabEnabled(6, False)
self.ui.tabWidget.setTabEnabled(7, False)
self.ui.tabWidget.setTabEnabled(8, False)
self.ui.tabWidget.setTabEnabled(9, False)
def __del__ (self):
self.ui = None
def closeEvent(self, event):
QtGui.QFrame.closeEvent(self, event)
self.savePreferences()
# Kill all processes that may still be running (stuck) or better, wait for them to complete
maxTimeToCompletion = 1000*60*20 # 20min in ms -> maximum duration for any thread (it will be killed after that)
qthr = [t for t in self.threads if isinstance(t, QtCore.QThread)]
thr = [t for t in self.threads if not isinstance(t, QtCore.QThread)]
print "Closing all qthreads"
unfinished = [t for t in qthr if not t.wait(maxTimeToCompletion)]
print "Killing %i QThreads still running"%len(unfinished)
[t.terminate() for t in unfinished]
def checkKill(p, timeout):
""" This function checks if the thread is still running.
If so, it waits until timeout (in ms), then kills it if it is still running"""
try:
print "Trying to kill "+repr(p)
t = 0
while(p.poll() is None and t < timeout):
time.sleep(5)
t = t + 5000
if p.poll() is None:
p.kill()
except:
pass
print "Closing all threads"
finished = [checkKill(t, maxTimeToCompletion) for t in thr]
print "Quitting BrainVisa"
axon.processes.cleanup()
print "Quit !"
QtGui.qApp.quit()
def initialize(self):
"""Reads the preference file, checks the available patients and sequences"""
#Localisation du fichier de preference
prefpath = os.path.join(os.path.expanduser('~'), '.imageimport')
# Chargement du fichier et stockage dans self.prefs
# Basic prefs
self.prefs = {'dicomOutputPath':os.path.join(os.path.expanduser('~'), 'dicomOut'),'niftiOutputPath':os.path.join(os.path.expanduser('~'), 'niftiOut'), 'sites':['Gre',]}
try:
if (os.path.exists(prefpath)):
filein = open(prefpath, 'rb')
#self.prefs = pickle.load(filein)
#fout.write(json.dumps({'mars_atlas':resection_mars_atlas_info}))
try:
self.prefs = json.loads(filein.read())
except:
filein.close()
filein = open(prefpath, 'rb')
self.prefs = pickle.load(filein)
filein.close()
except:
pass
self.dicomOutputPath = self.prefs['dicomOutputPath']
self.niftiOutputPath = self.prefs['niftiOutputPath']
if 'currentProtocol' in self.prefs:
self.currentProtocol = self.prefs['currentProtocol']
if 'currentSubject' in self.prefs:
self.currentSubject = self.prefs['currentSubject']
# Grenoble/Lyon/Other sites...
if 'sites' in self.prefs:
self.ui.subjectSiteCombo.clear()
self.ui.subjectSiteCombo.addItems(self.prefs['sites'])
#check what spm path has been precised in BrainVisa
configuration = Application().configuration
brainvisa_spm12_path = configuration.SPM.spm12_path
brainvisa_spm12_standalone_path = configuration.SPM.spm12_standalone_path
brainvisa_freesurfer_home_path = configuration.freesurfer._freesurfer_home_path
if 'spm' in self.prefs:
if brainvisa_spm12_path != self.prefs['spm']:
QtGui.QMessageBox.warning(self, u"SPM", u"SPM path different between IntrAnat and BrainVisa, strange, you should check that, by default keep the one precised in IntrAnat")
if os.path.isfile(self.prefs['spm']+os.sep+'Contents.m'):
op_cont = open(self.prefs['spm']+os.sep+'Contents.m')
line = op_cont.readline()
line = op_cont.readline()
spm_version = line.split(' ')[3]
if spm_version == '(SPM12)':
self.setSpmTemplatePath(self.prefs['spm']) #+os.sep+'toolbox/OldNorm/T1.nii')
elif spm_version == '(SPM8)':
QtGui.QMessageBox.warning(self, u"SPM", u"SPM version not supported anymore")
#self.setSpmTemplatePath(self.prefs['spm']) #+os.sep+'templates/T1.nii')
else:
QtGui.QMessageBox.warning(self, u"SPM", u"SPM version unknown")
else:
QtGui.QMessageBox.warning(self, u"SPM", u"SPM path is not defined in tab 'Préférences'\n Normalization and SPM coregistration won't work !")
else:
if len(configuration.SPM.spm12_path)>0:
print("used brainvisa spm path")
self.setSpmTemplatePath(brainvisa_spm12_path)
self.prefs['spm']=brainvisa_spm12_path
else:
QtGui.QMessageBox.warning(self, u"SPM", u"SPM path is not defined (or wrong) in tab 'Préférences'\n Normalization and SPM coregistration won't work !")
if 'spm_standalone' in self.prefs:
if brainvisa_spm12_standalone_path != self.prefs['spm_standalone']:
QtGui.QMessageBox.warning(self, u"SPM standalone", u"SPM standalone path different between IntrAnat and BrainVisa, strange, you should check that, by default keep the one precised in IntrAnat")
self.setSpmStandalonePath(self.prefs['spm_standalone'])
else:
self.setSpmStandalonePath(brainvisa_spm12_standalone_path)
if 'freesurfer' in self.prefs:
if brainvisa_freesurfer_home_path != self.prefs['freesurfer']:
QtGui.QMessageBox.warning(self, u"Freesurfer", u"Freesurfer path different between IntrAnat and BrainVisa, strange, you should check that, by default keep the one precised in IntrAnat")
self.setFreesurferPath(self.prefs['freesurfer'])
else:
self.setFreesurferPath(brainvisa_freesurfer_home_path)
if 'FileNoDBPath' in self.prefs:
self.setNoDBFilePath(self.prefs['FileNoDBPath'])
#self.prefs['freesurfer'] = str(self.ui.prefFreesurferEdit.text())
if 'ants' in self.prefs:
self.setANTsPath(self.prefs['ants'])
if 'coregisterMethod' in self.prefs:
self.coregMethod = self.prefs['coregisterMethod']
if self.coregMethod == 'ANTs':
self.ui.prefSPMcheckbox.setCheckState(False)
self.ui.prefANTScheckbox.setCheckState(True)
self.ui.prefAimscheckbox.setCheckState(False)
if self.coregMethod == 'spm':
self.ui.prefSPMcheckbox.setCheckState(True)
self.ui.prefANTScheckbox.setCheckState(False)
self.ui.prefAimscheckbox.setCheckState(False)
if self.coregMethod == 'Aims':
self.ui.prefSPMcheckbox.setCheckState(False)
self.ui.prefANTScheckbox.setCheckState(False)
self.ui.prefAimscheckbox.setCheckState(True)
if 'projectSelected' in self.prefs:
if self.prefs['projectSelected'] != []:
projects= [self.ui.radioButtonProject,self.ui.radioButtonProject_2,self.ui.radioButtonProject_3,self.ui.radioButtonProject_4]
projects[self.prefs['projectSelected'][0]].setChecked(True)
# Test if matlab is available
if 'matlabOk' not in self.prefs or self.prefs['matlabOk'] == False:
if matlabIsPresent():
self.prefs['matlabOk'] = True
else:
QtGui.QMessageBox.warning(self, u"Matlab", u"The command 'matlab' doesn't work !\nSPM coregistration and normalization won't work")
self.prefs['matlabOk'] = False
# Scanner les dossiers et séquences déjà importées, en faire un dictionnaire :
self.dicomOutContent = self.analyzeDicomOutput(self.dicomOutputPath)
self.niftiOutContent = self.analyzeNiftiOutput(self.niftiOutputPath)
def warningMEDIC(self):
shortwarning = TimerMessageBox(5,self)
shortwarning.exec_()
def savePreferences(self):
prefpath = os.path.join(os.path.expanduser('~'), '.imageimport')
self.prefs['dicomOutputPath'] = self.dicomOutputPath
self.prefs['niftiOutputPath'] = self.niftiOutputPath
self.prefs['currentProtocol'] = self.currentProtocol
self.prefs['currentSubject'] = self.currentSubject
self.prefs['sites'] = [str(self.ui.subjectSiteCombo.itemText(item)) for item in range(self.ui.subjectSiteCombo.count())]
if len(str(self.ui.prefSpmTemplateEdit.text()))>0:
self.prefs['spm'] = str(self.ui.prefSpmTemplateEdit.text())
else:
self.prefs.pop('spm',None)
if len(str(self.ui.prefANTsEdit.text()))>0:
self.prefs['ants']=str(self.ui.prefANTsEdit.text())
else:
self.prefs.pop('ants',None)
if len(str(self.ui.prefSpmStandaloneEdit.text()))>0:
self.prefs['spm_standalone'] = str(self.ui.prefSpmStandaloneEdit.text())
else:
self.prefs.pop('spm_standalone',None)
if len(str(self.ui.prefFreesurferEdit.text()))>0:
self.prefs['freesurfer'] = str(self.ui.prefFreesurferEdit.text())
else:
self.prefs.pop('freesurfer',None)
if len(str(self.ui.prefNoDBFileLocationEdit.text()))>0:
self.prefs['FileNoDBPath'] = str(self.ui.prefNoDBFileLocationEdit.text())
else:
self.prefs.pop('FileNoDBPath',None)
if self.ui.prefANTScheckbox.isChecked():
self.prefs['coregisterMethod'] = 'ANTs'
elif self.ui.prefSPMcheckbox.isChecked():
self.prefs['coregisterMethod'] = 'spm'
elif self.ui.prefAimscheckbox.isChecked():
self.prefs['coregisterMethod'] = 'Aims'
else:
self.prefs['coregisterMethod'] = 'spm'
self.coregMethod = self.prefs['coregisterMethod']
projects= [self.ui.radioButtonProject.isChecked(),self.ui.radioButtonProject_2.isChecked(),self.ui.radioButtonProject_3.isChecked(),self.ui.radioButtonProject_4.isChecked()]
project_selected = [x for x in range(len(projects)) if projects[x]==True]
self.prefs['projectSelected'] = project_selected
fileout = open(prefpath, 'wb')
pickle.dump(self.prefs, fileout)
#to modify to json
fileout.close()
def createItemDirs(self, item):
""" Create the directories containing the provided WriteDiskItem and insert them in the BrainVisa database """
# Copied from brainvisa.processes, in ExecutionContext._processExecution()
dirname = os.path.dirname( item.fullPath() )
dir=dirname
dirs = []
while not os.path.exists( dir ):
dirs.append(dir)
dir=os.path.dirname(dir)
if dirs:
try:
os.makedirs( dirname )
except OSError, e:
if not e.errno == errno.EEXIST:
# filter out 'File exists' exception, if the same dir has
# been created concurrently by another instance of BrainVisa
# or another thread
raise
for d in dirs:
dirItem=neuroHierarchy.databases.createDiskItemFromFileName(d, None)
def analyzeDicomOutput(self, root):
""" Structure of the dicom output directory is supposed to be
root/patient/sequence/dicomfiles.
This returns the dictionary of patients and sequences already imported in there"""
if not os.path.isdir(root):
return {}
return dict([(f, os.listdir(os.path.join(root, f))) for f in os.listdir(root) if os.path.isdir(os.path.join(root, f))])
def analyzeNiftiOutput(self, root):
""" Structure of the nifti output directory is supposed to be
root/patient/sequence.nii.
This returns the dictionary of patients and sequences already imported in there"""
if not os.path.isdir(root):
return {}
return dict([(f, [seq.split('.nii')[0] for seq in os.listdir(os.path.join(root, f))]) for f in os.listdir(root) if os.path.isdir(os.path.join(root, f))])
def storeImageReferentialsAndTransforms(self, image):
"""Stores referential and transformation files for an image from its headers -> native, scanner-based, coregistered to"""
# Notes : on prend le header de l'image, on crée un objet referentiel pour le référentiel natif,
# puis un pour chaque transformation définie dans le header
# On stocke les transfos entre le natif et chacun de ces référentiels à partir des infos du header.
# Comment alors faire pour lier le 'coregistered to blabla' au 'scanner based' d'une autre image ? Stocker une transfo identité ou utiliser copyReferential ?
# Et est-ce que copyReferential met à jour toutes les transfos stockées qui utilisaient le référentiel écrasé ?
# D'autre part, comment repérer le référentiel Scanner-based d'une image en particulier ? Pour créer la transfo t1post vers t1pre à partir du recalage SPM...
att = image.attributes()
refName = att['modality']+'_'+att['acquisition']
print "Storing refs/transfos for "+str(refName)
# Create a Referential object in the database to represent the native referential of the image
moda = self.modas[att['modality']]
nativeRef = self.transfoManager.referential(image)
if nativeRef is None:
print '...Creating native ref'
nativeRef = self.transfoManager.createNewReferentialFor(image, name = refName+'native', description = 'Native Anatomist Referential for ' + refName + ' image', referentialType='Referential of '+moda)
try:
neuroHierarchy.databases.createDiskItemFromFileName(os.path.dirname( nativeRef.fullPath() ))
except:
pass
# Create the scanner-based referential
#wdiScan = WriteDiskItem( 'Scanner Based Referential', 'Referential', exactType=True )
#refScan = wdiScan.findValue( image )
refScan = self.transfoManager.findOrCreateReferential('Scanner Based Referential', image, name = refName+'_Scanner-Based', description = 'Scanner-Based referential for ' + refName + ' image')
try:
neuroHierarchy.databases.createDiskItemFromFileName(os.path.dirname( refScan.fullPath() ))
except:
pass
if refScan is None:
print '...Creating scanner-based ref'
refScan = self.transfoManager.createNewReferentialFor(wdiScan, name = refName+'_Scanner-Based', description = 'Scanner-Based referential for ' + refName + ' image', referentialType='Scanner Based Referential')
try:
neuroHierarchy.databases.createDiskItemFromFileName(os.path.dirname( refScan.fullPath() ))
except:
pass
# Find where to store the scanner-base transformation
wdiTransformScan = WriteDiskItem( 'Transformation to Scanner Based Referential', 'Transformation matrix', exactType=True )
transformScan = wdiTransformScan.findValue(image)
# Read the header of the image and read all transformations available
f = aims.Finder()
f.check(image.fileName())
trs = list(f.header()['transformations'])
refs = list(f.header()['referentials'])
#print "ATTRIBUTES : "+repr(att)
trm_to_scannerBased = None
if ("Scanner-based anatomical coordinates" in refs ):
trm_to_scannerBased = trs[refs.index("Scanner-based anatomical coordinates")]
if trm_to_scannerBased is None:
print "No Scanner-based transfo in image header, using first available transfo instead."
try:
trm_to_scannerBased = trs[0]
except:
pass
if transformScan is None:
print "Cannot find path for Scanner-based transform in database -> transformation not stored !"
elif trm_to_scannerBased is None:
print "Cannot find Scanner-based transformation in header !"
else:
print '...storing scanner-based transfo'
#Store information into the trm file
mot = aims.Motion( trm_to_scannerBased )
image.setMinf('SB_Transform',str(trm_to_scannerBased))
aims.write( mot, transformScan.fullPath() )
try:
neuroHierarchy.databases.createDiskItemFromFileName(os.path.dirname( transformScan.fullPath() ))
except:
pass
#set and update database
print ".... setting transfo info : from %s to %s for %s"%(repr(nativeRef), repr(refScan), repr(transformScan))
self.transfoManager.setNewTransformationInfo( transformScan, source_referential=nativeRef, destination_referential= refScan)
def analyseBrainvisaDB(self, tab=None):
""" Analyze the BrainVisa Database to fill the data for the brainvisa and registration tab (provide the tab number to update only the chosen one, 0 or 4) """
rdi = ReadDiskItem( 'Center', 'Directory' )#, requiredAttributes={'center':'Epilepsy'} )
protocols = list( rdi._findValues( {}, None, False ) )
protocols = sorted([str(p.attributes()['center']) for p in protocols])
if len(protocols) == 0:
rep = QtGui.QMessageBox.warning(self, "Center (former protocol)", u"No center/protocole defined in BrainVisa Database !")
text, ok = QtGui.QInputDialog.getText(self, 'Input Dialog', 'Enter the name of the center/protocole:')
if (ok & bool(text)):
wdi = WriteDiskItem('Center', 'Directory' ) #'gz compressed NIFTI-1 image' )
di = wdi.findValue({'center' : str(text)})
os.mkdir(di.fullPath())
neuroHierarchy.databases.insertDiskItem( di, update=True )
if self.currentProtocol in protocols:
currentIndex = protocols.index(self.currentProtocol)
else:
currentIndex = 0
def selectSubj(subjCombo):
" Subfunction to select the current subject "
if self.currentSubject is None:
return
idx = subjCombo.findText(self.currentSubject)
print "search current subj"
if idx != -1:
print "found at "+repr(idx)
subjCombo.setCurrentIndex(idx)
if tab == 0 or tab is None: # Tab 0 is BrainVisa database tab
self.ui.bvProtocolCombo.clear()
self.ui.bvProtocolCombo.addItems(protocols)
self.ui.bvProtocolCombo.setCurrentIndex(currentIndex)
selectSubj(self.ui.bvSubjectCombo)
if tab == 1 or tab is None: # Tab 1 is Create Subject tab
self.ui.subjectProtocolCombo.clear()
self.ui.subjectProtocolCombo.addItems(protocols)
self.ui.subjectProtocolCombo.setCurrentIndex(currentIndex)
if tab == 3 or tab is None: # Tab 3 is Import Nifti tab
self.ui.niftiProtocolCombo.clear()
self.ui.niftiProtocolCombo.addItems(protocols)
self.ui.niftiProtocolCombo.setCurrentIndex(currentIndex)
selectSubj(self.ui.niftiSubjectCombo)
if tab == 7 or tab is None: # Tab 7 is Implantation tab
self.ui.implProtocolCombo.clear()
self.ui.implProtocolCombo.addItems(protocols)
self.ui.implProtocolCombo.setCurrentIndex(currentIndex)
selectSubj(self.ui.implSubjectCombo)
if tab == 4 or tab is None: # Tab 4 is Registration tab
self.ui.regProtocolCombo.clear()
self.ui.regProtocolCombo.addItems(protocols)
self.ui.regProtocolCombo.setCurrentIndex(currentIndex)
selectSubj(self.ui.regSubjectCombo)
if tab == 2 or tab is None: # Tab 2 is Patient Information tab
#pdb.set_trace()
#self.ui.patProtocolCombo.currentIndexChanged.disconnect(self._pathologyinfo)
self.ui.patProtocolCombo.clear()
self.ui.patProtocolCombo.addItems(protocols)
#self.connect(self.ui.patProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), lambda s:self.selectProtocol(s,self.ui.patSubjectCombo))
#self._pathologyinfo = pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)
#self.connect(self.ui.patProtocolCombo, QtCore.SIGNAL('currentIndexChanged(QString)'),self._pathologyinfo) #lambda :pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol))
self.ui.patProtocolCombo.setCurrentIndex(currentIndex)
self.pathologypatientInfo = pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)
selectSubj(self.ui.patSubjectCombo)
#pdb.set_trace()
#self.pathologypatientInfo = pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)
if tab == 6 or tab is None: # Tab 6 is SEEG tab
self.ui.seegProtocolCombo.clear()
self.ui.seegProtocolCombo.addItems(protocols)
self.ui.seegProtocolCombo.setCurrentIndex (currentIndex)
selectSubj(self.ui.seegSubjectCombo)
def selectProtocol(self, proto, comboToFillWithSubjects):
""" A BrainVisa protocol was selected : query the database to get the list of subjects and put them in the provided QComboBox"""
self.currentProtocol = str(proto)
rdi = ReadDiskItem( 'Subject', 'Directory', requiredAttributes={'center':str(proto)} )
subjects = list( rdi._findValues( {}, None, False ) )
comboToFillWithSubjects.clear()#self.ui.bvSubjectCombo.clear()
comboToFillWithSubjects.addItems(sorted([s.attributes()['subject'] for s in subjects]))
#if self.ui.tabWidget.currentIndex() ==2:
# self.pathologypatientInfo = pathologypatientinfo.buildUI(self.ui.patpatGroupBox,self.currentProtocol)
def setCurrentSubject(self, subj):
if not subj: # ignore empty values
return
print "current subj : "+str(subj)
self.currentSubject = str(subj)
def findAllImagesForSubject(self, protocol, subj):
""" Returns all images for a subject from the brainvisa database.
@return an array of ReadDiskItem
"""
rdi = ReadDiskItem( 'Raw T1 MRI', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images = list( rdi._findValues( {}, None, False ) )
images = [x for x in images if "skull_stripped" not in x.fullName()]
rdi = ReadDiskItem( 'T2 MRI', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'CT', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'PET', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'fMRI-epile', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'Statistic-Data', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'FLAIR', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'FreesurferAtlas', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'FGATIR', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
rdi = ReadDiskItem( 'HippoFreesurferAtlas', 'BrainVISA volume formats', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
images += list( rdi._findValues( {}, None, False ) )
return images
def selectBvSubject(self, subj):
""" A BrainVisa subject was selected : query the database to get the list of images"""
# Display "Date : XXXX-XX-XX - Seq: T1 - Acq : T1Pre
self.ui.bvImageList.clear()
images = self.findAllImagesForSubject(self.ui.bvProtocolCombo.currentText(), subj)
#name = modality + acquisition + subacquisition if exist subacquisition key else modality + acquisition
self.ui.bvImageList.addItems(sorted([i.attributes()['modality'] + ' - '+ i.attributes()['acquisition'] + ' - ' + i.attributes()['subacquisition'] if 'subacquisition' in i.attributes().keys()\
#i.attributes()['modality'] if 'acquisition' not in i.attributes().keys()\
else i.attributes()['modality'] + ' - '+ i.attributes()['acquisition'] for i in images ]))
dict_temporaire = {}
for i in images:
if 'subacquisition' in i.attributes().keys():
dict_temporaire.update({i.attributes()['modality'] + ' - ' + i.attributes()['acquisition'] + ' - ' + i.attributes()['subacquisition']:i.fileName()})
else:
dict_temporaire.update({i.attributes()['modality'] + ' - ' + i.attributes()['acquisition']:i.fileName()})
#self.bvImagePaths = dict((i.attributes()['modality'] + ' - ' + i.attributes()['acquisition'] + ' - ' + i.attributes()['subacquisition'], i.fileName() if 'subacquisition' in i.attributes().keys()\
#else i.attributes()['modality'] + ' - ' + i.attributes()['acquisition'], i.fileName() for i in images))
self.bvImagePaths = dict_temporaire
def selectBvImage(self, item):
""" A BrainVisa image was double-clicked : display it !"""
self.clearAnatomist()
path = self.bvImagePaths[str(item.text())]
mri = self.a.loadObject(path)
self.a.addObjects(mri, self.wins)
self.dispObj.append(mri)
def removeFromDB(self, file, db=None):
"""
If the file is a directory, recursive call to remove all its content before removing the directory.
Corresponding diskitem is removed from the database if it exists.
Taken from brainvisa-4.3.0/python/brainvisa/data/qt4gui/hierarchyBrowser.py
"""
if db is None:
try:
db=neuroHierarchy.databases.database(neuroHierarchy.databases.getDiskItemFromFileName(file).get("_database"))
except:
pass
if os.path.isdir(file):
for f in os.listdir(file):
self.removeFromDB(os.path.join(file, f), db)
os.rmdir(file)
else:
os.remove(file)
if db:
diskItem=db.getDiskItemFromFileName(file, None)
if diskItem:
db.removeDiskItem(diskItem)
def deleteBvSubject(self):
protocol = str(self.ui.bvProtocolCombo.currentText())
subj = str(self.ui.bvSubjectCombo.currentText())
rep = QtGui.QMessageBox.warning(self, u'Confirmation', u"<font color='red'><b>ATTENTION</b><br/>you are gonna Erase ALL subject datas<br/><b>DELETE THE SUBJECT%s ?</b></font>"%subj, QtGui.QMessageBox.Yes | QtGui.QMessageBox.No, QtGui.QMessageBox.No)
if rep == QtGui.QMessageBox.Yes:
print "Deleting subject %s"%subj
rdi = ReadDiskItem( 'Subject', 'Directory', requiredAttributes={'center':str(protocol), 'subject':str(subj) } )
di = list( rdi._findValues( {}, None, False ) )
if len(di) != 1:
print "%s subject(s) found ! Cannot delete if there is more than 1 !"%repr(len(di))
return
self.removeFromDB(di[0].fullPath(), neuroHierarchy.databases.database(di[0].get("_database")))
self.setStatus(u"Subject %s deleted from the database"%subj)
# Reset the list of subjects :
self.selectProtocol(str(self.ui.bvProtocolCombo.currentText()),self.ui.bvSubjectCombo)
def deleteBvImage(self):
#Delete the current acquisition (including transforms and segmentations : the full acquisition directory
imageName = None
try:
imageName = str(self.ui.bvImageList.currentItem().text())