v2.1a3 bugfix for crashes during dilation, add local debug tools to w…

…eb interface
kjamison · Oct 23, 2021 · acadc6c · acadc6c
1 parent fc00329
commit acadc6c
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Showing 3 changed files with 42 additions and 8 deletions.
diff --git a/website/config/nemo-version.json b/website/config/nemo-version.json
@@ -1,4 +1,4 @@
 {
-    "nemo_version": "2.1a2",
+    "nemo_version": "2.1a3",
     "nemo_version_date": "2021-10-22"
 }
diff --git a/website/config/nemo_startup.sh b/website/config/nemo_startup.sh
@@ -332,12 +332,14 @@ for o in $(echo ${output_prefix_list} | tr "," " "); do
                 #to get the filename with dilation
                 out_dilation_fmt=$(echo $atlasline | jq --raw-output '.parcfile_dilated_format //empty')
                 
-                if [ "${out_dilation_fmt}" = "compute" ] && [ "${out_dilation}" != "0" ]; then
-                    #Dilate the parcellation by x mm to make sure we catch nearby streamlines
-                    out_filename_dilated=$(echo ${out_filename} | sed -E 's#\.(NII|nii)(\.GZ|\.gz)?$##')_dil${out_dilation}.nii.gz
-                    echo "Dilating parcellation volume by ${out_dilation}mm. New parcellation: ${out_filename_dilated}"
-                    python dilate_parcellation.py -dilatemm ${out_dilation} ${out_filename} ${out_filename_dilated}
-                    out_filename=${out_filename_dilated}
+                if [ "${out_dilation_fmt}" = "compute" ]; then
+                    if [ "${out_dilation}" != "0" ]; then
+                        #Dilate the parcellation by x mm to make sure we catch nearby streamlines
+                        out_filename_dilated=$(echo ${out_filename} | sed -E 's#\.(NII|nii)(\.GZ|\.gz)?$##')_dil${out_dilation}.nii.gz
+                        echo "Dilating parcellation volume by ${out_dilation}mm. New parcellation: ${out_filename_dilated}"
+                        python dilate_parcellation.py -dilatemm ${out_dilation} ${out_filename} ${out_filename_dilated}
+                        out_filename=${out_filename_dilated}
+                    fi
                 elif [ "x${out_dilation_fmt}" != x ]; then
                     #this is used for pre-dilated subject-specific parcellations, ie fs86_dil%d_allsubj.npz
                     out_filename=${atlasdir}/$(printf ${out_dilation_fmt} ${out_dilation})

diff --git a/website/uploader.js b/website/uploader.js
@@ -211,9 +211,18 @@ function showUploader(run_internal_script) {
         extra_html+=['<input type="checkbox" id="debug" name="debug" value="1">',
         '<label for="debug">Run in debug mode</label><br/><br/>'].join('\n');
 
+        extra_html+=['<button id="add_all_atlases" onclick="addAllAtlases()">Add all atlases</button>',
+        '<button id="set_all_dilations0" onclick="setAllDilations(0)">Dilation 0</button>',
+        '<button id="set_all_dilations1" onclick="setAllDilations(1)">Dilation 1</button>',
+        '<button id="set_all_dilations2" onclick="setAllDilations(2)">Dilation 2</button>',
+        '<button id="set_all_dilations3" onclick="setAllDilations(3)">Dilation 3</button>',
+        '</br>'].join('\n');
+
         //For now, lets only offer this option for debugging purposes
         extra_accum_html=['<input type="checkbox" id="cumulative" name="cumulative" value="1">',
         '<label for="cumulative">Accumulate total hits along streamline (Much smaller ChaCo scores)</label><br/>'].join('\n');
+
+
     }
 
     extra_algo_html=['<label for="tracking_algorithm_select">Tractography algorithm:</label>',
@@ -267,7 +276,7 @@ function showUploader(run_internal_script) {
 
     var gittxt=" [<a class='gitlink' href='https://github.com/kjamison/nemo#readme' target='_blank'>github docs</a>]";
     //get version info
-    if(document.URL.startsWith("file:///")){
+    if(run_local_script){
         nemo_version_info={nemo_version: "LOCAL", nemo_version_date: "TODAY"};
         document.getElementById('version').innerHTML="NeMo vLOCAL"+gittxt;
     } else {
@@ -311,6 +320,29 @@ function neutralMessage(message,keep_buttons_disabled){
 }
 
 
+//Debugging functions
+function addAllAtlases(){
+    var parcsel_id="addparc_select";
+    var parcsel=document.getElementById(parcsel_id);
+    atlaslist=Object.keys(atlasinfo); 
+    for(var i=0; i<atlaslist.length; i++){
+        parcsel.value=atlaslist[i]; 
+        addOutput("parc",parcsel_id); 
+    }
+}
+function setAllDilations(dilation){
+    if(dilation===undefined)
+        dilation=3;
+
+    var nextparc=parseInt(getNextAvailableId("addparc",1).replace("addparc",""));
+    for(var i=1; i<nextparc; i++){
+        var dilsel=document.getElementById("addparc"+i+"_dilselect");
+        if(dilsel)
+            dilsel.value=dilation
+    }
+}
+
+
 function getTrackingAlgoSelectHtml(id){
     var htmlTemplate=['<select id="'+id+'" name="'+id+'">'];
     algonames=Object.keys(tracking_algo_info);