Merge pull request #436 from a3sha2/master

update regress report

core/report.py

@@ -296,15 +296,19 @@ def ulify(elements):
 
             #html_report=html_report + '<h1> prestats module </h1> <h3> Co-registration </h3> <p> Functional registration to Structural .</p> <object type="image/svg+xml" data="'+ fmreg+ '" alt="Segmentation" width="2000"height="800"></object>'
 
-    #elif i == 'regress':
+    elif i == 'regress':
          #not using it now but will be needed later i hope
-        # segm=outdir+'/prestats/'+prefix+'_segmentation.nii.gz'
-         #seg_data=load_img(segm).get_data()
-         #resid=outdir+'regress/'+prefix+'_residualised.nii.gz'
-         #tr=nib.load(resid).header['pixdim'][4]
-         #plot_carpet(img=resid,atlaslabels=seg_data,tr=tr,output_file=outdir+'/regress/'+prefix+'_residualized.svg')
-         #residplot='regress/'+prefix+'_residualized.svg'
-         #html_report=html_report + '<h1> regress module </h1> <h3> Residualized BOLD data </h3> <object type="image/svg+xml" data="'+ residplot +'" alt="Segmentation" width="1000"height="800"></object>'
+         segm=outdir+'/prestats/'+prefix+'_segmentation.nii.gz'
+         seg_data=load_img(segm).get_data()
+         resid=outdir+'regress/'+prefix+'_residualised.nii.gz'
+         tr=nib.load(resid).header['pixdim'][4]
+
+         plot_carpet(img=resid,atlaslabels=seg_data,tr=tr,
+                        output_file=outdir+'/regress/'+prefix+'_residualized.svg')
+
+         residplot='regress/'+prefix+'_residualized.svg'
+
+         html_report=html_report + '<h1> regress module </h1> <h3> Residualized BOLD data </h3> <object type="image/svg+xml" data="'+ residplot +'" alt="Segmentation" width="1000"height="800"></object>'
     elif i == 'fcon':
          filejson = outdir+'/'+prefix+'_atlas/'+prefix+'_atlas.json'
          with open(filejson, 'r') as atlasfile:

core/utils.py

@@ -449,7 +449,7 @@ def compose_view(bg_svgs, fg_svgs, ref=0, out_file='report.svg'):
 
     yoffset = 0
     for i, r in enumerate(roots):
-        r.moveto(0, yoffset)
+        r.moveto(0, yoffset,scale=scales[i])
         if i == (nsvgs - 1):
             yoffset = 0
         else:

xcpEngine

@@ -401,7 +401,7 @@ echo "generating report"
 for sub in ${!cohort[@]}
    do
    mkdir -p ${out[sub]}/figures
-   mv  $(ls -f ${out[sub]}/regress/*svg)  ${out[sub]}/figures/  2>/dev/null
+   #mv  $(ls -f ${out[sub]}/regress/*svg)  ${out[sub]}/figures/  2>/dev/null
    echo $standard >> ${out[sub]}/template.txt
    ##########################################################
    # remove previous html