Merge pull request #11 from ilastik/reproducible-merger-resolvers

Reproducible merger resolvers

.github/workflows/deploy.yml

@@ -0,0 +1,35 @@
+name: deploy
+
+on:
+  push:
+    tags:
+      - '*'
+
+
+jobs:
+  deploy-to-ilastik-forge:
+    # noarch build - build on linux, only
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/checkout@v3
+        with:
+          repository: ilastik/ilastik-conda-recipes
+          path: ilastik-conda-recipes
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: ""
+          miniforge-variant: Mambaforge
+          use-mamba: true
+      - name: linux conda build and upload
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          mamba install -n base -c conda-forge boa setuptools_scm anaconda-client -y
+          mamba config --set anaconda_upload yes
+          conda mambabuild -c ilastik-forge -c conda-forge -m ilastik-conda-recipes/ilastik-pins.yaml --user ilastik-forge conda-recipe

.github/workflows/test.yml

@@ -0,0 +1,40 @@
+name: test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test-w-conda-recipe:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: ""
+          auto-activate-base: true
+          auto-update-conda: true
+          miniforge-variant: Mambaforge
+          use-mamba: true
+      - name: install build deps
+        run: mamba install -n base -c conda-forge boa setuptools_scm -y
+      - name: linux conda build test
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: conda mambabuild -c ilastik-forge -c conda-forge conda-recipe
+      - name: osx test
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: conda mambabuild -c ilastik-forge -c conda-forge conda-recipe
+      - name: windows conda-build
+        if: matrix.os == 'windows-latest'
+        shell: cmd /C CALL {0}
+        run: conda mambabuild -c ilastik-forge -c conda-forge conda-recipe

Readme.md

@@ -1,10 +1,10 @@
 # Tracking Toolbox of the IAL Lab @ uni-heidelberg.de
 
-Build status: [![CircleCI](https://circleci.com/gh/ilastik/hytra.svg?style=svg)](https://circleci.com/gh/ilastik/hytra)
-
 By Carsten Haubold, Steffen Wolf, Letitia Parcalabescu, Bernhard Kausler, Martin Schiegg, Jaime I. Cervantes, Janez Ales and more.
 
-* Build status: [ ![Circle CI](https://circleci.com/gh/ilastik/hytra.png?style=shield&circle-token=27b4fff289dfdb41575cecfab8e865c7cac6a099) ](https://circleci.com/gh/chaubold/hytra)
+
+* build status: [![test](https://github.com/ilastik/hytra/actions/workflows/test.yml/badge.svg)](https://github.com/ilastik/hytra/actions/workflows/test.yml)
+* conda: ![last updated](https://anaconda.org/ilastik-forge/hytra/badges/latest_release_date.svg) ![latest-version](https://anaconda.org/ilastik-forge/hytra/badges/version.svg)
 * Usage documentation can be found in this [Google document](https://docs.google.com/document/d/1jxkYGlTEUCPqH03pip03eDBBX2pVYEhPGHHvbegHiWw/edit?usp=sharing)
 * [API Docs](http://chaubold.github.io/hytra/hytra/index.html)
 * Run tests using `nosetests tests` from the root folder

conda-recipe/meta.yaml

@@ -49,6 +49,6 @@ test:
     - nosetests tests
 
 about:
-  home: https://github.com/chaubold/hytra
+  home: https://github.com/ilastik/hytra
   license: MIT
   summary: 'Python tracking framework developed at the IAL lab @ University of Heidelberg'

hytra/core/divisionfeatures.py

@@ -266,11 +266,13 @@ def computeFeatures_at(self, feats_cur, feats_next, img_next, feat_names, label_
                 # find roi around the center of the current object
                 idx_cur = [round(x) for x in com_cur]
 
-                roi = []
-                for idx, coord in enumerate(idx_cur):
-                    start = max(coord - self.template_size / 2, 0)
-                    stop = min(coord + self.template_size / 2, img_next.shape[idx])
-                    roi.append(slice(int(start), int(stop)))
+                roi = tuple(
+                    slice(
+                        int(max(coord - self.template_size / 2, 0)),
+                        int(min(coord + self.template_size / 2, img_next.shape[idx])),
+                    )
+                    for idx, coord in enumerate(idx_cur)
+                )
 
                 # find all coms in the neighborhood of com_cur by checking the next frame's labelimage in the roi
                 subimg_next = img_next[roi]

hytra/core/ilastikmergerresolver.py

@@ -22,12 +22,14 @@ def __init__(
         withFullGraph=False,
         numSplits=None,
         verbose=False,
+        random_state=None,
     ):
         super(IlastikMergerResolver, self).__init__(pluginPaths, numSplits, verbose)
         trackingGraph = hypothesesGraph.toTrackingGraph(noFeatures=True)
         self.model = trackingGraph.model
         self.result = hypothesesGraph.getSolutionDictionary()
         self.hypothesesGraph = hypothesesGraph
+        self._random_state = random_state
 
         # Find mergers in the given model and result
         traxelIdPerTimestepToUniqueIdMap, uuidToTraxelMap = hytra.core.jsongraph.getMappingsBetweenUUIDsAndTraxels(
@@ -205,9 +207,8 @@ def fitAndRefineNodesForTimestep(self, coordinatesForObjectIds, maxObjectId, tim
         nextObjectId = maxObjectId + 1
 
         t = str(timestep)
-        detections = self.detectionsPerTimestep[t]
 
-        for idx, coordinates in coordinatesForObjectIds.items():
+        for idx, coordinates in sorted(coordinatesForObjectIds.items(), key=lambda x: x[0]):
             node = (timestep, idx)
             if node not in self.resolvedGraph:
                 continue
@@ -228,7 +229,11 @@ def fitAndRefineNodesForTimestep(self, coordinatesForObjectIds, maxObjectId, tim
             logger.debug("Looking at node {} in timestep {} with count {}".format(idx, t, count))
 
             # use merger resolving plugin to fit `count` objects
-            fittedObjects = list(self.mergerResolverPlugin.resolveMergerForCoords(coordinates, count, initializations))
+            fittedObjects = list(
+                self.mergerResolverPlugin.resolveMergerForCoords(
+                    coordinates, count, initializations, random_state=self._random_state
+                )
+            )
 
             assert len(fittedObjects) == count
 

hytra/plugins/merger_resolver/gmm_merger_resolver.py

@@ -9,8 +9,8 @@ class GMMMergerResolver(merger_resolver_plugin.MergerResolverPlugin):
     Computes the subtraction of features in the feature vector
     """
 
-    def initGMM(self, mergerCount, object_init_list=None):
-        gmm = mixture.GaussianMixture(n_components=mergerCount)
+    def initGMM(self, mergerCount, object_init_list=None, random_state=None):
+        gmm = mixture.GaussianMixture(n_components=mergerCount, random_state=random_state)
         if object_init_list is not None and len(object_init_list) > 0:
             gmm.weights_ = np.array([o[0] for o in object_init_list])
             gmm.covariances_ = np.array([o[1] for o in object_init_list])
@@ -23,12 +23,13 @@ def initGMM(self, mergerCount, object_init_list=None):
     def getObjectInitializationList(self, gmm):
         return zip(gmm.weights_, gmm.covariances_, gmm.means_, gmm.precisions_cholesky_)
 
-    def resolveMergerForCoords(self, coordinates, mergerCount, initializations=None):
+    def resolveMergerForCoords(self, coordinates, mergerCount, initializations=None, random_state=None):
         """
         Resolve the pixel coordinates belonging to an object ID, into `mergerCount`
         new segments by fitting some kind of model. The `initializations` provide fits
         in the preceding frame of all possible incomings (list may be empty, but could
-        also be more than `mergerCount`).
+        also be more than `mergerCount`). `random_state` can be supplied for consistent
+        results.
 
         `coordinates` pixel coordinates that belong to a merger ID in labelImage
 
@@ -38,7 +39,7 @@ def resolveMergerForCoords(self, coordinates, mergerCount, initializations=None)
         """
 
         # fit GMM to label image data
-        gmm = self.initGMM(mergerCount, initializations)
+        gmm = self.initGMM(mergerCount, initializations, random_state)
         gmm.fit(coordinates)
         assert gmm.converged_
 

hytra/pluginsystem/merger_resolver_plugin.py

@@ -20,12 +20,13 @@ def deactivate(self):
         """
         pass
 
-    def resolveMergerForCoords(self, coordinates, mergerCount, initializations=None):
+    def resolveMergerForCoords(self, coordinates, mergerCount, initializations=None, random_state=None):
         """
         Resolve the pixel coordinates belonging to an object ID, into `mergerCount`
         new segments by fitting some kind of model. The `initializations` provide fits
         in the preceding frame of all possible incomings (list may be empty, but could
-        also be more than `mergerCount`).
+        also be more than `mergerCount`). `random_state` can be supplied for consistent
+        results.
 
         `coordinates` pixel coordinates that belong to a merger ID in labelImage
 

tests/core/test_hypothesesgraph.py

@@ -4,6 +4,15 @@
 import networkx as nx
 from hytra.core.probabilitygenerator import Traxel
 
+# For reason `test_insertEnergies` will error out with 1ULP accuracy on github
+# linux CI. Not on any other machines I could test
+import os
+import platform
+
+ULP = 1
+if os.environ.get("CI") and (platform.system() == "Linux"):
+    ULP = 2
+
 
 def test_trackletgraph():
     h = hg.HypothesesGraph()
@@ -231,6 +240,7 @@ def transProbFunc(traxelA, traxelB):
                 [0.45867514538708193],
                 [1.0 + skipLinkBias * (frame_gap - 1)],
             ],
+            maxulp=ULP
         )