From 139df1685e77aed1f7a243e68b09dad8e54126ce Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Fri, 23 Jun 2017 12:08:39 -0700
Subject: [PATCH 1/6] enh: removing python generation part

---
 imports/api/module_tables.js     | 134 ++++++++++++----------
 imports/ui/module_templates.html | 124 +++++----------------
 imports/ui/module_templates.js   | 183 +++++++++----------------------
 3 files changed, 160 insertions(+), 281 deletions(-)

diff --git a/imports/api/module_tables.js b/imports/api/module_tables.js
index 26be6a2..ffa4d61 100644
--- a/imports/api/module_tables.js
+++ b/imports/api/module_tables.js
@@ -10,34 +10,58 @@ import "./methods.js"
 
 TabularTables = {}
 
+console.log("Meteor settings are", Meteor.settings)
 
+Meteor.settings.public.modules.forEach(function(mod, idx, arr){
+  TabularTables[mod.entry_type] = new Tabular.Table({
+    name: mod.entry_type,
+    collection: Subjects,
+    autoWidth: false,
+    columns: _.map(mod.fields, function(field){
+      switch (field.function_name) {
+        case "get_filter_field":
+          return get_filter_field(mod.entry_type, field.id, field.name)
+          break;
+        case "get_qc_viewer":
+          return get_qc_viewer(mod.entry_type, field.id, field.name)
+          break;
+        case "get_qc_filter_field":
+          return get_qc_filter_field(mod.entry_type, field.id, field.name)
+        default:
+          return {data: field.id, title: field.name}
+
+      }
+    })
+  })
+})
 
+/*
 TabularTables.demographic =  new Tabular.Table({
 name:"demographic",
     autoWidth: false,
     collection: Subjects,
     columns:[
-    
-      
+
+
         get_filter_field("demographic", "msid", "msid"),
-      
-    
-      
+
+
+
         get_filter_field("demographic", "subject_id", "Exam ID"),
-      
-    
-      
+
+
+
         get_filter_field("demographic", "Study Tag", "Study Tag"),
-      
-    
-      
+
+
+
         get_filter_field("demographic", "DCM_InstitutionName", "Site"),
-      
-    
-      
+
+
+
         get_filter_field("demographic", "metrics.DCM_InstitutionName", "Date"),
-      
-    
+
+
     ]
     })
 
@@ -47,31 +71,31 @@ name:"freesurfer",
     autoWidth: false,
     collection: Subjects,
     columns:[
-    
-      
+
+
         get_filter_field("freesurfer", "subject_id", "Exam ID"),
-      
-    
-      
+
+
+
         get_qc_viewer("freesurfer", "name", "Freesurfer ID"),
-      
-    
-      
+
+
+
         get_qc_filter_field("freesurfer", "quality_check.QC", "QC"),
-      
-    
-      
+
+
+
         get_filter_field("freesurfer", "checkedBy", "checked by"),
-      
-    
-      
+
+
+
         get_filter_field("freesurfer", "quality_check.user_assign", "Assigned To"),
-      
-    
-      
+
+
+
         {data: "quality_check.notes_QC", title: "Notes" }
-      
-    
+
+
     ]
     })
 
@@ -81,31 +105,31 @@ name:"test",
     autoWidth: false,
     collection: Subjects,
     columns:[
-    
-      
+
+
         get_filter_field("test", "subject_id", "Exam ID"),
-      
-    
-      
+
+
+
         get_qc_viewer("test", "name", "View Image"),
-      
-    
-      
+
+
+
         get_qc_filter_field("test", "quality_check.QC", "QC"),
-      
-    
-      
+
+
+
         get_filter_field("test", "checkedBy", "checked by"),
-      
-    
-      
+
+
+
         get_filter_field("test", "quality_check.user_assign", "Assigned To"),
-      
-    
-      
+
+
+
         {data: "quality_check.notes_QC", title: "Notes" }
-      
-    
+
+
     ]
     })
-
+*/
diff --git a/imports/ui/module_templates.html b/imports/ui/module_templates.html
index c8cfa9e..23d8a1a 100644
--- a/imports/ui/module_templates.html
+++ b/imports/ui/module_templates.html
@@ -1,129 +1,63 @@
 <template name="base">
 
 
-    {{> demographic }}
-
-    {{> freesurfer }}
-
-    {{> test }}
-
-
-</template>
-
-
-<template name="demographic">
-
-<h1 id="Exams">Exams</h1>
-
-    <button class="btn btn-default btn-sm" type="button" data-toggle="collapse" data-target="#collapseExample" aria-expanded="true" aria-controls="collapseExample">
-      Toggle Calendar
-    </button>
-    <br>
-    <br>
-    <div class="collapse in" id="collapseExample" aria-labelledby="collapseExample">
-        <div id="d3vis_date_demographic"></div>
-    </div>
-
-
-
-
-    <div id="demographic_table">
-
-        {{> tabular table=TabularTables.demographic selector=selector class="table table-striped table-bordered table-condensed"}}
-
-    </div>
-
-</template>
-
-
-<template name="freesurfer">
-
-<h1 id="Freesurfer">Freesurfer</h1>
-
- <br>
-  <br>
-    Selected Metric: {{currentMetric}}
-  <div class="d3board">
-
-        <svg id="d3vis_freesurfer"></svg>
-
-  </div>
-
-    <select id="metric-select-freesurfer" class="form-control">
-    <option disabled="disabled" selected="selected" >Please Select</option>
-    {{#each metric}}
-        <option value="{{this}}">{{this}}</option>
+    {{#each modules}}
+      {{> Template.dynamic template="module" data=this}}
     {{/each}}
-</select>
-
-  <br><br>
-
-
-
-
-    <div id="freesurfer_table">
-
-        {{> tabular table=TabularTables.freesurfer selector=selector class="table table-striped table-bordered table-condensed"}}
-
-    </div>
 
 </template>
 
+<template name="module">
 
-<template name="test">
+  <h1 id="{{this.name}}">{{this.name}}</h1>
 
-<h1 id="Test">Test</h1>
-
- <br>
-  <br>
+  {{#if histogram}}
     Selected Metric: {{currentMetric}}
-  <div class="d3board">
-
-        <svg id="d3vis_test"></svg>
 
-  </div>
+    <div class="d3board">
+       <svg id="d3vis_{{this.entry_type}}"></svg>
+    </div>
 
-    <select id="metric-select-test" class="form-control">
+    <select id="metric-select" class="form-control">
     <option disabled="disabled" selected="selected" >Please Select</option>
     {{#each metric}}
         <option value="{{this}}">{{this}}</option>
     {{/each}}
-</select>
-
-  <br><br>
+    </select>
 
+  {{/if}}
 
+  {{#if date_histogram}}
 
+    <button class="btn btn-default btn-sm" type="button" data-toggle="collapse" data-target="#collapseExample" aria-expanded="true" aria-controls="collapseExample">
+      Toggle Calendar
+    </button>
+    <br>
+    <br>
+    <div class="collapse in" id="collapseExample" aria-labelledby="collapseExample">
+        <div id="d3vis_date_{{entry_type}}"></div>
+    </div>
 
-    <div id="test_table">
+  {{/if}}
 
-        {{> tabular table=TabularTables.test selector=selector class="table table-striped table-bordered table-condensed"}}
+  {{> tabular table=table selector=selector class="table table-striped table-bordered table-condensed"}}
 
-    </div>
 
 </template>
 
-
-
 <template name="body_sidebar">
 
   <div class="span3">
             <div class="bs-docs-sidebar">
 
                     <ul class="nav nav-list bs-docs-sidenav affix">
-                        
-                        <li><a href="#Exams">
-                            <span class="badge badge-inverse"></span> Exams</a>
-                        </li>
-                        
-                        <li><a href="#Freesurfer">
-                            <span class="badge badge-inverse"></span> Freesurfer</a>
-                        </li>
-                        
-                        <li><a href="#Test">
-                            <span class="badge badge-inverse"></span> Test</a>
+
+                      {{#each modules}}
+                        <li><a href="#{{this.name}}">
+                            <span class="badge badge-inverse"></span> {{this.name}}</a>
                         </li>
-                        
+                      {{/each}}
+
                     </ul>
 
                  <ul class="nav nav-list affix qbox">
@@ -170,4 +104,4 @@ <h5>Saved Queries</h5>
             </div>
         </div>
 
-</template>
\ No newline at end of file
+</template>
diff --git a/imports/ui/module_templates.js b/imports/ui/module_templates.js
index 5adc82b..d5d6b2e 100644
--- a/imports/ui/module_templates.js
+++ b/imports/ui/module_templates.js
@@ -48,7 +48,6 @@ render_histogram = function(entry_type){
                 var metric = Session.get("current_"+entry_type)//"Amygdala"
                 if (metric == null){
                     var all_metrics = Session.get(entry_type+"_metrics")
-
                     if (all_metrics != null){
                         Session.set("current_"+entry_type, all_metrics[0])
                     }
@@ -59,7 +58,7 @@ render_histogram = function(entry_type){
                     var filter = get_filter(entry_type)
                     //console.log("filter is", filter)
                     Meteor.call("getHistogramData", entry_type, metric, 20, filter, function(error, result){
-                    //console.log("result is", result)
+
                     var data = result["histogram"]
                     var minval = result["minval"]
                     var maxval = result["maxval"]
@@ -76,143 +75,65 @@ render_histogram = function(entry_type){
 }
 
 
+Template.base.helpers({
+  modules: function(){
+    console.log(Meteor.settings.public.modules)
+    return Meteor.settings.public.modules
+  }
+})
 
-Template.demographic.rendered = function() {
+Template.module.helpers({
+  selector: function(){
+    return get_filter(this.entry_type)
+  },
+  table: function(){
+    return TabularTables[this.entry_type]
+  },
+  histogram: function(){
+    return this.graph_type == "histogram"
+  },
+  date_histogram: function(){
+    return this.graph_type == "datehist"
+  },
+  metric: function(){
+          return get_metrics(this.entry_type)
+      },
+  currentMetric: function(){
+          return Session.get("current_"+this.entry_type)
+      }
+})
 
-      if (!this.rendered){
-        this.rendered = true
-         }
+Template.module.events({
+ "change #metric-select": function(event, template){
+     var metric = $(event.currentTarget).val()
+     console.log("metric: ", metric)
+     Session.set("current_"+this.entry_type, metric)
+ }
+})
 
+Template.base.rendered = function(){
+  if (!this.rendered){
+      this.rendered = true
+  }
 
-    
-      this.autorun(function() {
+  this.autorun(function() {
+      Meteor.settings.public.modules.forEach(function(self, idx, arr){
+        if (self.graph_type == "histogram"){
+          console.log("rendering histogram", self.entry_type)
+          render_histogram(self.entry_type)
+        }
+        else if (self.graph_type == "datehist") {
           Meteor.call("getDateHist", function(error, result){
-              do_d3_date_histogram(result, "#d3vis_date_demographic")
+              do_d3_date_histogram(result, "#d3vis_date_"+self.entry_type)
               })
-
+        }
       })
+  });
+}
 
-     
-
-  }
-
-
-
-
-
-Template.freesurfer.rendered = function() {
-
-      if (!this.rendered){
-        this.rendered = true
-         }
-
-
-    
-
-       this.autorun(function() {
-                render_histogram("freesurfer")
-
-       }); //end autorun
-
-     
-
-  }
-
-
-
-
-
-Template.test.rendered = function() {
-
-      if (!this.rendered){
-        this.rendered = true
-         }
-
-
-    
-
-       this.autorun(function() {
-                render_histogram("test")
-
-       }); //end autorun
-
-     
 
+Template.body_sidebar.helpers({
+  modules: function(){
+    return Meteor.settings.public.modules
   }
-
-
-
-
-
-
-
-Template.demographic.helpers({
-
-selector: function(){return get_filter("demographic")},
-
-
-
-})
-
-
-
-Template.freesurfer.helpers({
-
-selector: function(){return get_filter("freesurfer")},
-
-
-
-metric: function(){
-        return get_metrics("freesurfer")
-    },
-currentMetric: function(){
-        return Session.get("current_freesurfer")
-    }
-
-
-
 })
-
-
-
-Template.test.helpers({
-
-selector: function(){return get_filter("test")},
-
-
-
-metric: function(){
-        return get_metrics("test")
-    },
-currentMetric: function(){
-        return Session.get("current_test")
-    }
-
-
-
-})
-
-
-
-
-  
-
-  
-   Template.freesurfer.events({
-    "change #metric-select-freesurfer": function(event, template){
-        var metric = $(event.currentTarget).val()
-        console.log("metric: ", metric)
-        Session.set("current_freesurfer", metric)
-    }
-   })
-  
-
-  
-   Template.test.events({
-    "change #metric-select-test": function(event, template){
-        var metric = $(event.currentTarget).val()
-        console.log("metric: ", metric)
-        Session.set("current_test", metric)
-    }
-   })
-  

From 27884db2cdf4aa95b07da0380b4d22cc07c48bdb Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Fri, 23 Jun 2017 12:09:36 -0700
Subject: [PATCH 2/6] fix: added important settings.json file

---
 settings.json | 83 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 settings.json

diff --git a/settings.json b/settings.json
new file mode 100644
index 0000000..025aff1
--- /dev/null
+++ b/settings.json
@@ -0,0 +1,83 @@
+{
+  "public": {
+    "startup_json":"https://dl.dropboxusercontent.com/s/vnohn5nh9ho3j8a/data_rf.json?dl=0",
+    "modules": [
+    {"name": "Exams",
+      "entry_type": "demographic",
+    "fields": [
+      {"function_name": "get_filter_field",
+        "id": "msid",
+        "name": "msid"
+      },
+      {"function_name": "get_filter_field",
+        "id": "subject_id",
+        "name": "Exam ID"
+      },
+      {"function_name": "get_filter_field",
+        "id": "Study Tag",
+        "name": "Study Tag"
+      },
+      {"function_name": "get_filter_field",
+        "id": "DCM_InstitutionName",
+        "name": "Site"
+      },
+      {"function_name": "get_filter_field",
+        "id": "metrics.DCM_InstitutionName",
+        "name": "Date"
+      }
+    ],
+    "graph_type":"datehist",
+    "showgraph": true},
+      {
+        "name": "Freesurfer",
+        "entry_type": "freesurfer",
+        "fields": [
+          {
+            "function_name": "get_filter_field",
+            "id": "subject_id",
+            "name": "Exam ID"
+          },
+          {
+            "function_name": "get_qc_viewer",
+            "id": "name",
+            "name": "Freesurfer ID"
+          },
+          {
+            "function_name": "get_qc_filter_field",
+            "id": "quality_check.QC",
+            "name": "QC"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "checkedBy",
+            "name": "checked by"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "quality_check.user_assign",
+            "name": "Assigned To"
+          },
+          {
+            "function_name": null,
+            "id": "quality_check.notes_QC",
+            "name": "Notes"
+          }
+        ],
+        "graph_type": "histogram",
+        "colormaps": {
+          "0":{"name": "Grayscale",
+              "alpha": 1,
+              "min": 0,
+              "max": 255
+          },
+          "1": {
+            "name": "custom.Freesurfer",
+            "alpha": 0.5
+          }
+        },
+        "staticURL": "https://dl.dropboxusercontent.com/u/9020198/data/",
+        "usePeerJS": true
+      }
+  ]
+  }
+}

From 70315797536373e54eb91e880df09f01840609ce Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Fri, 23 Jun 2017 12:23:25 -0700
Subject: [PATCH 3/6] fix: removed any generator refs

---
 imports/startup/fill_empty_db.js |  21 +++---
 imports/ui/qc.js                 | 125 +++++++++++++++----------------
 settings.json                    |   1 +
 3 files changed, 73 insertions(+), 74 deletions(-)

diff --git a/imports/startup/fill_empty_db.js b/imports/startup/fill_empty_db.js
index dec564f..460b1c2 100644
--- a/imports/startup/fill_empty_db.js
+++ b/imports/startup/fill_empty_db.js
@@ -3,25 +3,24 @@ import {Subjects} from "../api/module_tables.js"
 if (Meteor.isServer) {
   // This code only runs on the server
   // Only publish tasks that are public or belong to the current user
-  
-  
+
+
  Meteor.startup(function () {
     //Subjects.remove({})
     //console.log("in metero startup function")
     if (Subjects.find().count() === 0) {
         //load the json from here: https://www.dropbox.com/s/enb5zemvmu2oqgw/data.json?dl=0
         //console.log(JSON.parse(HTTP.get("http:///private/generator.json").content))
-        myjson = JSON.parse(Assets.getText("generator.json"));
-        console.log("myjson", myjson["startup_json"])
-        var source_json = myjson["startup_json"] //"https://dl.dropboxusercontent.com/s/vnohn5nh9ho3j8a/data_rf.json?dl=0"
+        source_json = Meteor.settings.public.startup_json //JSON.parse(Assets.getText("generator.json"));
         //console.log(HTTP.get(source_json).content)
         myobject = JSON.parse(HTTP.get(source_json).content)
         //console.log("my object is", myobject.length)
-        myobject.forEach(function(val,idx,array){
-            Subjects.insert(val)
-        })
-        
+        if (Meteor.settings.load_if_empty){
+          myobject.forEach(function(val,idx,array){
+              Subjects.insert(val)
+          })
+        }
     }
   });
-  
-  }
+
+}
diff --git a/imports/ui/qc.js b/imports/ui/qc.js
index c778e11..d18da1f 100644
--- a/imports/ui/qc.js
+++ b/imports/ui/qc.js
@@ -15,8 +15,6 @@ import "./painter.js"
 use_peerJS = true
 
 
-
-
 addNewDrawing= function(template){
 
      //console.log("in add new drawing")
@@ -66,7 +64,8 @@ function arraysEqual(a, b) {
 
 var addPapaya = function(data, entry_type, template_instance, callback){
     //if (papayaContainers.length == 0){
-    Meteor.call("get_generator", entry_type, function(err, res){
+    //Meteor.call("get_generator", entry_type, function(err, res){
+    var res = _.find(Meteor.settings.public.modules, function(x){return x.entry_type == entry_type})
         var params = {}
         params["images"] = []
         var loadableImages = []
@@ -93,7 +92,7 @@ var addPapaya = function(data, entry_type, template_instance, callback){
             console.log("papayacontainers is", papayaContainers.pop())
         }
 
-        
+
 
             var cmap = res.colormaps
             if (cmap){
@@ -117,8 +116,8 @@ var addPapaya = function(data, entry_type, template_instance, callback){
                     else{
                         params[split_name] = {lut: opts.name, alpha: opts.alpha, min: opts.min, max:opts.max}
                     }
-    
-    
+
+
                 }
             }
             console.log("params is", params)
@@ -129,9 +128,9 @@ var addPapaya = function(data, entry_type, template_instance, callback){
                                             //callback()
                                             })
             papaya.Container.allowPropagation = true;
-            papayaContainers[0].viewer.mindcontrol_template = template_instance//Template.instance()
+            papayaContainers[0].viewer.mindcontrol_template = template_instance //Template.instance()
 
-        })
+        //})
 
 
 
@@ -159,7 +158,7 @@ var load_hotkeys = function(template_instance){
     contextHotkeys.add({
                     combo : "d d",
                     callback : function(){
-                        
+
                         var currMode = template_instance.logMode.get()
                         if (currMode == "contour"){
                             var contours = template_instance.contours.get()
@@ -173,20 +172,20 @@ var load_hotkeys = function(template_instance){
                             template_instance.contours.set(contours)
                             papayaContainers[0].viewer.drawViewer(true)
                         }
-                        
+
                         else if (currMode == "point"){
-                            
+
                         }
-                        
+
                         else if (currMode == "paint"){
                             //TODO: undo painting when you have time.
                             var painters = template_instance.painters.get()
                             var currPaint = painters.pop()
                             restore_vals(currPaint)
                             template_instance.painters.set(painters)
-                            
+
                         }
-                        
+
                     }
                 })
 
@@ -209,25 +208,25 @@ var load_hotkeys = function(template_instance){
                             currMode ="paint"
                         }
                         else if (currMode == "paint"){
-                            currMode = "point"   
+                            currMode = "point"
                         }
                         template_instance.logMode.set(currMode)
                     }
                 })
-    
+
     contextHotkeys.add({
                     combo : "z z",
                     callback : function(){
                         console.log("you want to hide the last overlay")
                         idx = papayaContainers[0].viewer.screenVolumes.length - 1
                         var isHidden = papayaContainers[0].viewer.screenVolumes[idx].hidden
-                        
+
                         if (!isHidden){papaya.Container.hideImage(0, idx)}
                         else{papaya.Container.showImage(0, idx)}
                         //papaya.Container.showImage(0, imageIndex)
                     }
-                })            
-                
+                })
+
     contextHotkeys.load()
 }
 
@@ -244,7 +243,7 @@ var sync_templates_decorator = function(template_instance){ return function(data
     var data = JSON.parse(data)
     //console.log("you want to sync a template w/ data", data)
     //console.log("template_instance is", template_instance)
-    
+
     if (data["action"] == "insert"){
         for (var key in data["data"]){
             var current = template_instance[key].get()
@@ -258,12 +257,12 @@ var sync_templates_decorator = function(template_instance){ return function(data
             }
             //console.log("current is", current)
             template_instance[key].set(current)
-            
+
         }
-        
+
     }
-    
-    
+
+
     if (data["action"] == "update"){
         for (var key in data["data"]){
             //console.log("you want to update entry in", key, "with uuid", data["data"][key]["uuid"])
@@ -278,9 +277,9 @@ var sync_templates_decorator = function(template_instance){ return function(data
         }
     }
     papayaContainers[0].viewer.drawViewer(true)
-    
 
-    
+
+
 }}
 
 
@@ -295,7 +294,7 @@ Template.view_images.onCreated(function(){
     this.painters = new ReactiveVar([])
     this.connections = {}
     Meteor.subscribe("presences")
-    
+
     if (use_peerJS){
         window.peer = new Peer({
           key: 'fqw6u5vy67n1att9',  // get a free key at http://peerjs.com/peerserver
@@ -303,12 +302,12 @@ Template.view_images.onCreated(function(){
           config: {'iceServers': [
             { url: 'stun:stun.l.google.com:19302' },
             { url: 'stun:stun1.l.google.com:19302' },
-          ]}    
+          ]}
         });
-        
+
         peer.on('open', function () {
           console.log("peer ID is", peer.id);
-          
+
           var current_profile = Meteor.users.findOne({_id: Meteor.userId()}).profile
           if (!current_profile){
               current_profile = {}
@@ -321,20 +320,20 @@ Template.view_images.onCreated(function(){
             }})
             console.log("profile si", Meteor.users.findOne({_id: Meteor.userId()}).profile)
         });
-        
+
         //TODO: sometimes this is null??? Then where do we set the listener?
         var my_template = this
-        
+
         peer.on("connection", function(conn){
             console.log("conn is", conn)
             conn.on("data", sync_templates_decorator(my_template))
-            
+
         });
     }
 
-    
-    
-    
+
+
+
 })
 
 
@@ -345,45 +344,45 @@ Template.view_images.helpers({
         Meteor.subscribe('userList')
         return Meteor.users.find({}).fetch()
     },
-    
+
     peerUsers: function(){
-      
-      if (use_peerJS){  
+
+      if (use_peerJS){
           var userIds = Presences.find().map(function(presence) {return presence.userId;});
           // exclude the currentUser
           var name = get_qc_name()
-    
+
           var template_instance = Template.instance()
           var to_return =  Meteor.users.find({_id: {$in: userIds, $ne: Meteor.userId()}});
-          
+
           if (to_return.count){
             var conns = get_open_connections(this)
             if (!conns.length){
-                
-                
+
+
                 var dude = Meteor.users.findOne({_id: {$in: userIds, $ne: Meteor.userId()}})
                 if (dude){
                 console.log("there are no connections but there is another person out there, so i'm connecting now", dude.username)
                 var conn = peer.connect(dude.profile[name])
                 conn.on("data", sync_templates_decorator(template_instance))
                 }
-                
+
             }
-            
+
             console.log("a peerjs connection exists, now we add a listener")
             for(var i = 0; i<conns.length; i++){
                 conns[i].on("data", sync_templates_decorator(template_instance))
             }
-            
+
           }
-    
+
           if (to_return == null){
               return []
           }
           return to_return
       }
       else{return 0}
-      
+
     },
 
     loggedPoints: function(){
@@ -546,9 +545,9 @@ Template.view_images.helpers({
             return to_display
         }
     },
-    
+
     loadPainter: function(){
-        return Session.get("reloadPainter")   
+        return Session.get("reloadPainter")
     }
 })
 
@@ -676,7 +675,7 @@ Template.view_images.events({
      template.loggedPoints.set(points)
      papayaContainers[0].viewer.drawViewer(true)
      send_to_peers({"action": "remove", "data":{"loggedPoints": this}})
-     
+
      //fill_all(template)
  },
  "click .remove-contour": function(event, template){
@@ -759,15 +758,15 @@ Template.view_images.events({
     console.log("you want to load", this)
     papaya.Container.addImage(0, this.absolute_path)
  },
- 
+
  'input #paintValue': function (event, template) {
     Session.set("paintValue", event.currentTarget.value);
   },
-  
+
   "click #paintEraser": function(event, template){
       Session.set("paintValue", 0)
   },
-  
+
   "click #paintPicker": function(event, template){
     var viewer = papayaContainers[0].viewer
     var N = viewer.screenVolumes.length
@@ -777,9 +776,9 @@ Template.view_images.events({
     var offset = ori.convertIndexToOffset(papayaRoundFast(c.x),papayaRoundFast(c.y),papayaRoundFast(c.z))
     Session.set("paintValue", vol.imageData.data[offset])
   },
-  
+
   "click #loadPainter": function(event, template){
-      
+
       var qc = Session.get("currentQC")
       var output = Subjects.findOne({entry_type: qc.entry_type, name: qc.name},{check_masks:1, _id:0, name:1, loggedPoints: 1, contours: 1})
       if (output){
@@ -789,12 +788,12 @@ Template.view_images.events({
                 var after_load = papayaload_callback(output)
                 after_load()
                 Session.set("reloadPainter", false)
-            }            
+            }
         }
       };
-    
+
   }
-  
+
 
 })
 
@@ -843,12 +842,12 @@ Template.view_images.rendered = function(){
                         Session.set("reloadPainter", true)
                     }
                 }
-                
-                
-                
+
+
+
                 addPapaya(output, qc.entry_type, Template.instance())
                 load_hotkeys(Template.instance())
-                
+
                 //get_config()
             }
 
diff --git a/settings.json b/settings.json
index 025aff1..512a38e 100644
--- a/settings.json
+++ b/settings.json
@@ -1,6 +1,7 @@
 {
   "public": {
     "startup_json":"https://dl.dropboxusercontent.com/s/vnohn5nh9ho3j8a/data_rf.json?dl=0",
+    "load_if_empty": true,
     "modules": [
     {"name": "Exams",
       "entry_type": "demographic",

From b285b26df1c26f8d544807f3edf9634558bf549e Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Fri, 23 Jun 2017 12:27:01 -0700
Subject: [PATCH 4/6] fix: removed generator for python

---
 private/generator.json | 1 -
 1 file changed, 1 deletion(-)
 delete mode 120000 private/generator.json

diff --git a/private/generator.json b/private/generator.json
deleted file mode 120000
index 4b98e66..0000000
--- a/private/generator.json
+++ /dev/null
@@ -1 +0,0 @@
-../imports/python_generate/generator.json
\ No newline at end of file

From 51f92f9180631d09193d4a287d9018640c76aec6 Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Fri, 23 Jun 2017 12:28:30 -0700
Subject: [PATCH 5/6] fix: removed python templates

---
 .../python_generate/generate_mindcontrol.py   |  31 ----
 imports/python_generate/generator.json        | 120 ---------------
 imports/python_generate/module_tables.js.tmpl |  30 ----
 .../module_templates.html.tmpl                | 112 --------------
 .../python_generate/module_templates.js.tmpl  | 141 ------------------
 5 files changed, 434 deletions(-)
 delete mode 100644 imports/python_generate/generate_mindcontrol.py
 delete mode 100644 imports/python_generate/generator.json
 delete mode 100644 imports/python_generate/module_tables.js.tmpl
 delete mode 100644 imports/python_generate/module_templates.html.tmpl
 delete mode 100644 imports/python_generate/module_templates.js.tmpl

diff --git a/imports/python_generate/generate_mindcontrol.py b/imports/python_generate/generate_mindcontrol.py
deleted file mode 100644
index bf0a174..0000000
--- a/imports/python_generate/generate_mindcontrol.py
+++ /dev/null
@@ -1,31 +0,0 @@
-__author__ = 'akeshavan'
-from jinja2 import Environment, FileSystemLoader
-import simplejson as json
-import os
-
-def load_json(filename):
-    with open(filename,'r') as fp:
-        data=json.load(fp)
-    return data
-
-files_to_generate = [{"filename": "module_tables.js.tmpl", "location":"../api/"},
-                     {"filename": "module_templates.js.tmpl", "location":"../ui/"},
-                     {"filename": "module_templates.html.tmpl", "location": "../ui/"}]
-
-env = Environment(loader=FileSystemLoader('./'))
-info = load_json("generator.json")
-
-for f in files_to_generate:
-    template = env.get_template(f["filename"])
-    outfile = os.path.join(f["location"], f["filename"].replace(".tmpl",""))
-    print("writing", outfile)
-    with open(outfile, "w") as q:
-        q.write(template.render(**info))
-#print(template.render(**info))
-
-"""
-template = env.get_template("module_templates.js.tmpl")
-#print(template.render(**info))
-template = env.get_template("module_templates.html.tmpl")
-print(template.render(**info))
-"""
\ No newline at end of file
diff --git a/imports/python_generate/generator.json b/imports/python_generate/generator.json
deleted file mode 100644
index e72bb7a..0000000
--- a/imports/python_generate/generator.json
+++ /dev/null
@@ -1,120 +0,0 @@
-{"start_tag":"{{",
-  "end_tag":"}}",
-  "startup_json":"https://dl.dropboxusercontent.com/s/vnohn5nh9ho3j8a/data_rf.json?dl=0",
-  "modules": [
-  {"name": "Exams",
-    "entry_type": "demographic",
-  "fields": [
-    {"function_name": "get_filter_field",
-      "id": "msid",
-      "name": "msid"
-    },
-    {"function_name": "get_filter_field",
-      "id": "subject_id",
-      "name": "Exam ID"
-    },
-    {"function_name": "get_filter_field",
-      "id": "Study Tag",
-      "name": "Study Tag"
-    },
-    {"function_name": "get_filter_field",
-      "id": "DCM_InstitutionName",
-      "name": "Site"
-    },
-    {"function_name": "get_filter_field",
-      "id": "metrics.DCM_InstitutionName",
-      "name": "Date"
-    }
-  ],
-  "graph_type":"datehist",
-  "showgraph": true},
-    {
-      "name": "Freesurfer",
-      "entry_type": "freesurfer",
-      "fields": [
-        {
-          "function_name": "get_filter_field",
-          "id": "subject_id",
-          "name": "Exam ID"
-        },
-        {
-          "function_name": "get_qc_viewer",
-          "id": "name",
-          "name": "Freesurfer ID"
-        },
-        {
-          "function_name": "get_qc_filter_field",
-          "id": "quality_check.QC",
-          "name": "QC"
-        },
-        {
-          "function_name": "get_filter_field",
-          "id": "checkedBy",
-          "name": "checked by"
-        },
-        {
-          "function_name": "get_filter_field",
-          "id": "quality_check.user_assign",
-          "name": "Assigned To"
-        },
-        {
-          "function_name": null,
-          "id": "quality_check.notes_QC",
-          "name": "Notes"
-        }
-      ],
-      "graph_type": "histogram",
-      "colormaps": {
-        "0":{"name": "Grayscale",
-            "alpha": 1,
-            "min": 0,
-            "max": 255
-        },
-        "1": {
-          "name": "custom.Freesurfer",
-          "alpha": 0.5
-        }
-      },
-      "staticURL": "https://dl.dropboxusercontent.com/u/9020198/data/",
-      "usePeerJS": true
-    },
-{
-      "name": "Test",
-      "entry_type": "test",
-      "fields": [
-        {
-          "function_name": "get_filter_field",
-          "id": "subject_id",
-          "name": "Exam ID"
-        },
-        {
-          "function_name": "get_qc_viewer",
-          "id": "name",
-          "name": "View Image"
-        },
-        {
-          "function_name": "get_qc_filter_field",
-          "id": "quality_check.QC",
-          "name": "QC"
-        },
-        {
-          "function_name": "get_filter_field",
-          "id": "checkedBy",
-          "name": "checked by"
-        },
-        {
-          "function_name": "get_filter_field",
-          "id": "quality_check.user_assign",
-          "name": "Assigned To"
-        },
-        {
-          "function_name": null,
-          "id": "quality_check.notes_QC",
-          "name": "Notes"
-        }
-      ],
-      "graph_type": "histogram",
-      "staticURL": "http://localhost:3002/",
-      "usePeerJS": false
-    }
-]}
diff --git a/imports/python_generate/module_tables.js.tmpl b/imports/python_generate/module_tables.js.tmpl
deleted file mode 100644
index 5ee1310..0000000
--- a/imports/python_generate/module_tables.js.tmpl
+++ /dev/null
@@ -1,30 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-import { Mongo } from 'meteor/mongo';
-import { check } from 'meteor/check';
-
-export const Subjects = new Mongo.Collection('subjects');
-
-import "./table_utils.js"
-import "./publications.js"
-import "./methods.js"
-
-TabularTables = {}
-
-{% for module in modules %}
-
-TabularTables.{{module.entry_type}} =  new Tabular.Table({
-name:"{{module.entry_type}}",
-    autoWidth: false,
-    collection: Subjects,
-    columns:[
-    {% for field in module.fields %}
-      {% if field.function_name %}
-        {{field.function_name}}("{{module.entry_type}}", "{{field.id}}", "{{field.name}}"),
-      {% else %}
-        {data: "{{field.id}}", title: "{{field.name}}" }
-      {% endif %}
-    {% endfor %}
-    ]
-    })
-{% endfor %}
-
diff --git a/imports/python_generate/module_templates.html.tmpl b/imports/python_generate/module_templates.html.tmpl
deleted file mode 100644
index 5f7aa3a..0000000
--- a/imports/python_generate/module_templates.html.tmpl
+++ /dev/null
@@ -1,112 +0,0 @@
-<template name="base">
-
-{% for module in modules %}
-    {{start_tag}}> {{module.entry_type}} {{end_tag}}
-{% endfor %}
-
-</template>
-
-{% for module in modules %}
-<template name="{{module.entry_type}}">
-
-<h1 id="{{module.name}}">{{module.name}}</h1>
-{% if module.graph_type == "datehist" %}
-    <button class="btn btn-default btn-sm" type="button" data-toggle="collapse" data-target="#collapseExample" aria-expanded="true" aria-controls="collapseExample">
-      Toggle Calendar
-    </button>
-    <br>
-    <br>
-    <div class="collapse {% if module.showgraph %}in{% endif %}" id="collapseExample" aria-labelledby="collapseExample">
-        <div id="d3vis_date_{{module.entry_type}}"></div>
-    </div>
-
-{% elif module.graph_type=="histogram"%}
- <br>
-  <br>
-    Selected Metric: {{start_tag}}currentMetric{{end_tag}}
-  <div class="d3board">
-
-        <svg id="d3vis_{{module.entry_type}}"></svg>
-
-  </div>
-
-    <select id="metric-select-{{module.entry_type}}" class="form-control">
-    <option disabled="disabled" selected="selected" >Please Select</option>
-    {{start_tag}}#each metric{{end_tag}}
-        <option value="{{start_tag}}this{{end_tag}}">{{start_tag}}this{{end_tag}}</option>
-    {{start_tag}}/each{{end_tag}}
-</select>
-
-  <br><br>
-
-{% endif %}
-
-
-    <div id="{{module.entry_type}}_table">
-
-        {{start_tag}}> tabular table=TabularTables.{{module.entry_type}} selector=selector class="table table-striped table-bordered table-condensed"{{end_tag}}
-
-    </div>
-
-</template>
-
-{% endfor %}
-
-<template name="body_sidebar">
-
-  <div class="span3">
-            <div class="bs-docs-sidebar">
-
-                    <ul class="nav nav-list bs-docs-sidenav affix">
-                        {% for module in modules%}
-                        <li><a href="#{{module.name}}">
-                            <span class="badge badge-inverse"></span> {{module.name}}</a>
-                        </li>
-                        {% endfor %}
-                    </ul>
-
-                 <ul class="nav nav-list affix qbox">
-                 <h5>Query Box</h5>
-
-  <button class="btn btn-default btn-small reset"> Reset </button>
-                     <br><br>
-
-
-                 <div class="well">
-
-                     {{start_tag}}#each currentSelector{{end_tag}}
-                    <span class="tag label label-info">
-                      <span class="{{start_tag}}this.mapper{{end_tag}}">{{start_tag}}this.name{{end_tag}}</span>
-                      <a><i class="remove glyphicon glyphicon-remove-sign glyphicon-white"></i></a>
-                    </span>
-                    <br><br>
-                     {{start_tag}}/each{{end_tag}}
-
-
-                 </div>
-<form class="form-inline">
-    <div class="form-group">
-        <button class="btn btn-default btn-small save"> Save </button>
-        <input type="text" name="qname" id="qname" class="form-control"><br>
-    </div>
-</form>
-                <h5>Saved Queries</h5>
-
-
-                {{start_tag}}#each savedQueries{{end_tag}}
-
-                    <span class="tag label label-primary">
-                      <span class="query {{name}}">{{start_tag}}name{{end_tag}}</span>
-                        <a><i class="removequery glyphicon glyphicon-trash glyphicon-white"></i></a>
-                    </span>
-
-                    <br>
-                    <br>
-
-                {{start_tag}}/each{{end_tag}}
-
-                 </ul>
-            </div>
-        </div>
-
-</template>
\ No newline at end of file
diff --git a/imports/python_generate/module_templates.js.tmpl b/imports/python_generate/module_templates.js.tmpl
deleted file mode 100644
index e549f49..0000000
--- a/imports/python_generate/module_templates.js.tmpl
+++ /dev/null
@@ -1,141 +0,0 @@
-import { Meteor } from 'meteor/meteor';
-import { Template } from 'meteor/templating';
-
-import './module_templates.html';
-import "./d3_plots.js"
-
-
-get_filter = function(entry_type){
-
- var globalSelector = Session.get("globalSelector")
-    var myselect = {}
-    myselect["entry_type"] = entry_type
-
-    if (globalSelector){
-        globalKeys = Object.keys(globalSelector)
-        //console.log("global keys are", globalKeys, globalKeys.indexOf(entry_type))
-        if (globalKeys.indexOf(entry_type) >= 0){
-            var localKeys = Object.keys(globalSelector[entry_type])
-            //console.log("local keys are", localKeys)
-            for (i=0;i<localKeys.length;i++){
-                myselect[localKeys[i]] = globalSelector[entry_type][localKeys[i]]
-            }//end for
-        };//end if
-
-        //console.log("selector for", entry_type, "is", myselect)
-
-        // In this part, if another filter has filtered subjects, then filter on the rest
-        var subselect = Session.get("subjectSelector")
-
-        if (subselect["subject_id"]["$in"].length){
-            myselect["subject_id"] = subselect["subject_id"]
-        }
-        //console.log("myselect is", myselect)
-        return myselect
-    }
-
-
-}
-
-get_metrics = function(entry_type){
-    Meteor.call("get_metric_names", entry_type, function(error, result){
-            Session.set(entry_type+"_metrics", result)
-        })
-        return Session.get(entry_type+"_metrics")
-}
-
-render_histogram = function(entry_type){
-                var metric = Session.get("current_"+entry_type)//"Amygdala"
-                if (metric == null){
-                    var all_metrics = Session.get(entry_type+"_metrics")
-
-                    if (all_metrics != null){
-                        Session.set("current_"+entry_type, all_metrics[0])
-                    }
-
-                }
-
-                if (metric != null){
-                    var filter = get_filter(entry_type)
-                    //console.log("filter is", filter)
-                    Meteor.call("getHistogramData", entry_type, metric, 20, filter, function(error, result){
-                    //console.log("result is", result)
-                    var data = result["histogram"]
-                    var minval = result["minval"]
-                    var maxval = result["maxval"]
-                    if (data.length){
-                        do_d3_histogram(data, minval, maxval, metric, "#d3vis_"+entry_type, entry_type)
-                    }
-                    else{
-                        console.log("attempt to clear histogram here")
-                    }
-
-
-                    });
-                }
-}
-
-{% for module in modules%}
-
-Template.{{module.entry_type}}.rendered = function() {
-
-      if (!this.rendered){
-        this.rendered = true
-         }
-
-
-    {% if module.graph_type == "datehist"%}
-      this.autorun(function() {
-          Meteor.call("getDateHist", function(error, result){
-              do_d3_date_histogram(result, "#d3vis_date_{{module.entry_type}}")
-              })
-
-      })
-
-     {% elif module.graph_type == "histogram" %}
-
-       this.autorun(function() {
-                render_histogram("{{module.entry_type}}")
-
-       }); //end autorun
-
-     {% endif %}
-
-  }
-
-
-
-{% endfor %}
-
-{% for module in modules%}
-
-Template.{{module.entry_type}}.helpers({
-
-selector: function(){return get_filter("{{module.entry_type}}")},
-
-{% if module.graph_type == "histogram" %}
-
-metric: function(){
-        return get_metrics("{{module.entry_type}}")
-    },
-currentMetric: function(){
-        return Session.get("current_{{module.entry_type}}")
-    }
-
-{% endif %}
-
-})
-
-{% endfor %}
-
-{% for module in modules %}
-  {% if module.graph_type == "histogram" %}
-   Template.{{module.entry_type}}.events({
-    "change #metric-select-{{module.entry_type}}": function(event, template){
-        var metric = $(event.currentTarget).val()
-        console.log("metric: ", metric)
-        Session.set("current_{{module.entry_type}}", metric)
-    }
-   })
-  {% endif %}
-{% endfor %}
\ No newline at end of file

From 2bfec89f45842a891b207d256f6ceb724986a0ad Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Fri, 23 Jun 2017 12:52:23 -0700
Subject: [PATCH 6/6] fix: added new freesurfer settings file, and fixed the
 style a little bit

---
 client/main.css          |   7 +-
 settings_freesurfer.json | 158 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 163 insertions(+), 2 deletions(-)
 create mode 100644 settings_freesurfer.json

diff --git a/client/main.css b/client/main.css
index 1428942..7ea230b 100644
--- a/client/main.css
+++ b/client/main.css
@@ -2,6 +2,11 @@ body {
   padding-top: 50px;
 }
 
+#metric-select {
+  margin-bottom: 10px;
+  margin-top: 10px;
+}
+
 .container {
     margin-left: 300px
 }
@@ -368,5 +373,3 @@ h4 td, th{
     color: #333;
     white-space: nowrap;
     }
-
-
diff --git a/settings_freesurfer.json b/settings_freesurfer.json
new file mode 100644
index 0000000..a964f1f
--- /dev/null
+++ b/settings_freesurfer.json
@@ -0,0 +1,158 @@
+{
+  "public": {
+    "startup_json":"https://dl.dropboxusercontent.com/s/vnohn5nh9ho3j8a/data_rf.json?dl=0",
+    "modules": [
+    {
+        "name": "Brainmask",
+        "entry_type": "brainmask",
+        "fields": [
+          {
+            "function_name": "get_filter_field",
+            "id": "subject_id",
+            "name": "Exam ID"
+          },
+          {
+            "function_name": "get_qc_viewer",
+            "id": "name",
+            "name": "Freesurfer ID"
+          },
+          {
+            "function_name": "get_qc_filter_field",
+            "id": "quality_check.QC",
+            "name": "QC"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "checkedBy",
+            "name": "checked by"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "quality_check.user_assign",
+            "name": "Assigned To"
+          },
+          {
+            "function_name": null,
+            "id": "quality_check.notes_QC",
+            "name": "Notes"
+          }
+        ],
+        "graph_type": "histogram",
+        "colormaps": {
+          "0":{"name": "Grayscale",
+              "alpha": 1,
+              "min": 0,
+              "max": 255
+          },
+          "1": {
+            "name": "Red Overlay",
+            "alpha": 0.2,
+            "min": 0,
+            "max": 2000
+          }
+        },
+        "staticURL": "http://localhost:3002/",
+        "usePeerJS": true
+      },
+  {
+        "name": "White Matter",
+        "entry_type": "wm",
+        "fields": [
+          {
+            "function_name": "get_filter_field",
+            "id": "subject_id",
+            "name": "Exam ID"
+          },
+          {
+            "function_name": "get_qc_viewer",
+            "id": "name",
+            "name": "Freesurfer ID"
+          },
+          {
+            "function_name": "get_qc_filter_field",
+            "id": "quality_check.QC",
+            "name": "QC"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "checkedBy",
+            "name": "checked by"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "quality_check.user_assign",
+            "name": "Assigned To"
+          },
+          {
+            "function_name": null,
+            "id": "quality_check.notes_QC",
+            "name": "Notes"
+          }
+        ],
+        "graph_type": "histogram",
+        "colormaps": {
+          "0":{"name": "Grayscale",
+              "alpha": 1,
+              "min": 0,
+              "max": 255
+          },
+          "1": {
+            "name": "Spectrum",
+            "alpha": 0.5
+          }
+        },
+        "staticURL": "http://localhost:3002/",
+        "usePeerJS": true
+      },
+  {
+        "name": "Segmentation",
+        "entry_type": "aparcaseg",
+        "fields": [
+          {
+            "function_name": "get_filter_field",
+            "id": "subject_id",
+            "name": "Exam ID"
+          },
+          {
+            "function_name": "get_qc_viewer",
+            "id": "name",
+            "name": "Freesurfer ID"
+          },
+          {
+            "function_name": "get_qc_filter_field",
+            "id": "quality_check.QC",
+            "name": "QC"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "checkedBy",
+            "name": "checked by"
+          },
+          {
+            "function_name": "get_filter_field",
+            "id": "quality_check.user_assign",
+            "name": "Assigned To"
+          },
+          {
+            "function_name": null,
+            "id": "quality_check.notes_QC",
+            "name": "Notes"
+          }
+        ],
+        "graph_type": "histogram",
+        "colormaps": {
+          "0":{"name": "Grayscale",
+              "alpha": 1,
+              "min": 0,
+              "max": 255
+          },
+          "1": {
+            "name": "custom.Freesurfer",
+            "alpha": 0.5
+          }
+        },
+        "staticURL": "http://localhost:3002/",
+        "usePeerJS": true
+      }]
+}
+}