Merge pull request #438 from a3sha2/master

update the report

.vscode/settings.json

@@ -1,2 +1,4 @@
 {
-    "restructuredtext.confPath": "${workspaceFolder}/docs",}
+    "restructuredtext.confPath": "${workspaceFolder}/docs",
+    "python.pythonPath": "/Users/adebimpe/anaconda3/bin/python",
+}

Dockerfile

@@ -60,10 +60,7 @@ RUN conda install -y python=3.7.1 \
     conda build purge-all; sync && \
     conda clean -tipsy && sync
 
-RUN  pip install --no-cache-dir nipype nibabel niworkflows nilearn==0.6.0 matplotlib 
-RUN  pip install --no-cache-dir numpy pandas traits scikit-learn 
-RUN  rm -rf ~/.cache/pip/* && sync
-RUN  apt-get update
+
 
 ENV FSLDIR="/opt/fsl-5.0.10" \
     PATH="/opt/fsl-5.0.10/bin:$PATH"
@@ -224,6 +221,11 @@ RUN sed -i '$iexport PATH=$PATH:$XCPEDIR' $ND_ENTRYPOINT
 
 RUN echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
 
+RUN  pip install --no-cache-dir nipype nibabel niworkflows==1.1.10 nilearn==0.6.0 matplotlib 
+RUN  pip install --no-cache-dir numpy pandas traits scikit-learn svgutils==0.3.1
+RUN  rm -rf ~/.cache/pip/* && sync
+RUN  apt-get update
+
 ADD . /xcpEngine
 
 # template 
@@ -266,5 +268,4 @@ RUN bash -c 'cp /xcpEngine/utils/license.txt /opt/freesurfer/'
 RUN bash -c '/xcpEngine/xcpReset'
 
 
-
 ENTRYPOINT ["/xcpEngine/xcpEngine"]

core/report.py

@@ -296,19 +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]
+         #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')
+         #plot_carpet(img=resid,atlaslabels=seg_data,tr=tr,
+                        #output_file=outdir+'/regress/'+prefix+'_residualized.svg')
 
-         residplot='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>'
+         #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

@@ -447,13 +447,13 @@ def compose_view(bg_svgs, fg_svgs, ref=0, out_file='report.svg'):
     # any element (used the first here) and the sum of heights
     fig = svgt.SVGFigure(width, heights[:nsvgs].sum())
 
-    yoffset = 0
-    for i, r in enumerate(roots):
-        r.moveto(0, yoffset,scale=scales[i])
-        if i == (nsvgs - 1):
-            yoffset = 0
-        else:
-            yoffset += heights[i]
+    #yoffset = 0
+    #for i, r in enumerate(roots):
+        #r.moveto(0, yoffset,scale=scales[i])
+        #if i == (nsvgs - 1):
+            #yoffset = 0
+        #else:
+            #yoffset += heights[i]
 
     # Group background and foreground panels in two groups
     if fg_svgs: