0.0.12; algofix

reality · Oct 5, 2021 · c7bbd4d · c7bbd4d
1 parent 8cd1164
commit c7bbd4d
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Showing 4 changed files with 26 additions and 19 deletions.
diff --git a/klarigi/build.gradle b/klarigi/build.gradle
@@ -88,4 +88,4 @@ jacocoTestReport {
   }
 }
 
-version = '0.0.12-SNAPSHOT'
+version = '0.0.12'
diff --git a/klarigi/src/main/groovy/klarigi/App.groovy b/klarigi/src/main/groovy/klarigi/App.groovy
@@ -38,6 +38,7 @@ class App {
       _ longOpt: 'min-exclusion', 'Min exclusion to use in stepdown algorithm. Default: 0.3', args: 1
       _ longOpt: 'max-total-inclusion', 'Max total inclusion to use in stepdown algorithm. Default: 0.95 (probably don\'t want to edit this one)', args: 1
       _ longOpt: 'step', 'Step by which to reduce coefficients in stepdown algorithm. Default: 0.05', args: 1
+      _ longOpt: 'debug', 'Print some debug output', type: Boolean
 
       _ longOpt: 'power', 'Use modification of algorithm which uses normalised power instead of inc/exc', type: Boolean
 
@@ -91,11 +92,11 @@ class App {
           System.exit(1)
         }
 
-        allExplanations = k.explainClusters(groups, o['output-scores'], o['power'], threads)
+        allExplanations = k.explainClusters(groups, o['output-scores'], o['power'], threads, o['debug'])
       } else if(o['group'] && o['group'] != '*') {
-        allExplanations = k.explainClusters([o['group']], o['output-scores'], o['power'], threads)
+        allExplanations = k.explainClusters([o['group']], o['output-scores'], o['power'], threads, o['debug'])
       } else {
-        allExplanations = k.explainAllClusters(o['output-scores'], o['power'], threads)
+        allExplanations = k.explainAllClusters(o['output-scores'], o['power'], threads, o['debug'])
       }
 
       allExplanations.each {

diff --git a/klarigi/src/main/groovy/klarigi/Klarigi.groovy b/klarigi/src/main/groovy/klarigi/Klarigi.groovy
@@ -157,7 +157,7 @@ public class Klarigi {
     }
   }
 
-  def explainCluster(cid, powerMode, outputScores, threads) {
+  def explainCluster(cid, powerMode, outputScores, threads, debug) {
     def scorer = new Scorer(ontoHelper, data)
     def candidates = scorer.scoreClasses(cid, threads)
 
@@ -173,21 +173,21 @@ public class Klarigi {
 
     // TODO: now we have to, ah, add the multiprocessing
     if(powerMode) {
-      StepDown.RunNewAlgorithm(coefficients, cid, candidates, data)
+      StepDown.RunNewAlgorithm(coefficients, cid, candidates, data, debug)
     } else {
-      StepDown.Run(coefficients, cid, candidates, data)
+      StepDown.Run(coefficients, cid, candidates, data, debug)
     }
   }
 
-  def explainClusters(groups, outputScores, powerMode, threads) {
+  def explainClusters(groups, outputScores, powerMode, threads, debug) {
     data.groupings.findAll { g, v -> groups.contains(g) }.collect { g, v ->
-      [ cluster: g, results: explainCluster(g, powerMode, outputScores, threads) ]
+      [ cluster: g, results: explainCluster(g, powerMode, outputScores, threads, debug) ]
     }
   }
 
-  def explainAllClusters(outputScores, powerMode, threads) {
+  def explainAllClusters(outputScores, powerMode, threads, debug) {
     data.groupings.collect { g, v ->
-      [ cluster: g, results: explainCluster(g, powerMode, outputScores, threads) ]
+      [ cluster: g, results: explainCluster(g, powerMode, outputScores, threads, debug) ]
     }
   }
 

diff --git a/klarigi/src/main/groovy/klarigi/StepDown.groovy b/klarigi/src/main/groovy/klarigi/StepDown.groovy
@@ -1,7 +1,7 @@
 package klarigi
 
 public class StepDown {
-  static def Run(c, cid, candidates, data) {
+  static def Run(c, cid, candidates, data, debug) {
     def totalCoverage = 0
     def stepDown = { e, icCutoff, exclusionCutoff, inclusionCutoff, totalInclusionCutoff ->
       while(totalCoverage <= (totalInclusionCutoff*100)) {
@@ -15,10 +15,13 @@ public class StepDown {
         if(data.groupings.size() > 1) {
           totalExclusion = (1-(((ef.collect { it.internalExcluded }.flatten().unique(false).size()) / (data.groupings.collect {k,v->v.size()}.sum() - data.groupings[cid].size()))))*100
         }
-        //println "DEBUG: running with ic cutoff: $icCutoff exclusion cutoff: $exclusionCutoff inclusion cutoff: $inclusionCutoff total: coverage: $totalCoverage/$totalInclusionCutoff"
-        if(totalCoverage <= (totalInclusionCutoff*100)) {
+        if(debug) {
+          println "DEBUG: running with ic cutoff: $icCutoff exclusion cutoff: $exclusionCutoff inclusion cutoff: $inclusionCutoff total: coverage: $totalCoverage/$totalInclusionCutoff"
+        }
+        if(totalCoverage < (totalInclusionCutoff*100)) {
+          totalCoverage = 0 // OMG
           if(inclusionCutoff <= c.MIN_INCLUSION) {
-            if(icCutoff >= c.MIN_IC) {
+            if(icCutoff > c.MIN_IC) {
               icCutoff -= c.STEP
               exclusionCutoff = c.MAX_EXCLUSION
               inclusionCutoff = c.MAX_INCLUSION
@@ -46,7 +49,7 @@ public class StepDown {
     return stepDown(candidates, c.MAX_IC, c.MAX_EXCLUSION, c.MAX_INCLUSION, c.MAX_TOTAL_INCLUSION)
   }
 
-  static def RunNewAlgorithm(c, cid, candidates, data) {
+  static def RunNewAlgorithm(c, cid, candidates, data, debug) {
     def totalCoverage = 0
     def stepDown = { e, icCutoff, powerCutoff, totalInclusionCutoff ->
       while(totalCoverage <= (totalInclusionCutoff*100)) {
@@ -60,10 +63,13 @@ public class StepDown {
         if(data.groupings.size() > 1) {
           totalExclusion = (1-(((ef.collect { it.internalExcluded }.flatten().unique(false).size()) / (data.groupings.collect {k,v->v.size()}.sum() - data.groupings[cid].size()))))*100
         }
-        //println "DEBUG: running with ic cutoff: $icCutoff exclusion cutoff: $exclusionCutoff inclusion cutoff: $inclusionCutoff total: coverage: $totalCoverage/$totalInclusionCutoff"
-        if(totalCoverage <= (totalInclusionCutoff*100)) {
+        if(debug) {
+          println "DEBUG: running with ic cutoff: $icCutoff exclusion cutoff: $exclusionCutoff inclusion cutoff: $inclusionCutoff total: coverage: $totalCoverage/$totalInclusionCutoff"
+        }
+        if(totalCoverage < (totalInclusionCutoff*100)) {
+          totalCoverage = 0
           if(powerCutoff <= c.MIN_POWER) {
-            if(icCutoff >= c.MIN_IC) {
+            if(icCutoff > c.MIN_IC) {
               icCutoff -= c.STEP
               powerCutoff = c.MAX_POWER
               continue;
-Original file line number
+Diff line change
@@ Expand Up / @@ -88,4 +88,4 @@ jacocoTestReport { @@
       }
     }
-    version = '0.0.12-SNAPSHOT'
+    version = '0.0.12'