SleePyPhases 0.8.2__tar.gz → 0.8.4__tar.gz

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SleePyPhases
-Version: 0.8.2
+Version: 0.8.4
 Summary: A framwork for creating deep learning pipelines for sleep data
 Home-page: https://gitlab.com/sleep-is-all-you-need/sleepyphases
 Author: Franz Ehrlich

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases/config.yaml

@@ -163,5 +163,6 @@ predict:
   inputFile: null
   channelMapping: {}
   weights: null
+pretraining: {}
 
 inputShape: null

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases/phases/BuildDataset.py

@@ -42,12 +42,19 @@ class BuildDataset(Phase):
 
                 dm = self.getData("dataversionmanager", DataversionManager)
                 metadata = self.project.getData("metadata", pd.DataFrame)
+                channelMetaData = self.project.getData("metadata-channels", pd.DataFrame)
                 metadataMap = {r["recordId"]: r for r in metadata.iloc}
                 allRecordIds = [r for subgroup in dm.unShuffledgroupedRecords.values() for r in subgroup]
-
                 recordIds = dm.getRecordsForSplit(splitName)
                 recordIndexes = [allRecordIds.index(r) for r in recordIds]
-                recordMetadata = [metadataMap[r] for r in allRecordIds] # unshuffled
+
+                if len(channelMetaData) > 0:
+                    recordMetadata = [
+                        {**metadataMap[r].to_dict(), "channels": channelMetaData[channelMetaData["recordId"] == r]}
+                        for r in allRecordIds
+                    ]
+                else:
+                    recordMetadata = [metadataMap[r] for r in allRecordIds]
 
                 # handle segment wise data
                 recordLengthsInSegments = None

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases/phases/EvalPlotExamples.py

@@ -3,7 +3,6 @@ import numpy as np
 from pyPhases import Phase
 from pyPhasesRecordloader import RecordSignal, Signal
 
-from SleePyPhases.Plot import Plot
 from SleePyPhases.DataManipulation import DataManipulation
 from datetime import timedelta
 
@@ -37,6 +36,8 @@ class EvalPlotExamples(Phase):
         self, recordSignal: RecordSignal, fileName, sliceValues=None, highlights=None, offset=0, title="Example"
     ):
         from matplotlib import pyplot as plt
+        from SleePyPhases.Plot import Plot
+
         samplingrate = recordSignal.targetFrequency
         paddingInS = self.examplePaddingInS
         padding = paddingInS * samplingrate

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases/phases/EvalReport.py

@@ -8,7 +8,6 @@ import yaml
 from pyPhases import Phase
 from pyPhasesRecordloader import RecordSignal, Signal
 
-from SleePyPhases import Plot
 from SleePyPhases.DataManipulation import DataManipulation
 
 
@@ -51,6 +50,7 @@ class EvalReport(Phase):
     def plotRecordSignal(
         self, label, classExamples, recordSignal: RecordSignal, fileName, sliceValues=None, highlights=None, offset=0, classNames=None, threshold=None, labelName=""
     ):
+        from SleePyPhases import Plot
 
         classificationNames = {}
         for i, name1 in enumerate(classNames):
@@ -217,6 +217,7 @@ class EvalReport(Phase):
 
         
         metrics = self.getConfig("trainingParameter.validationMetrics")
+        metrics = [metrics] if isinstance(metrics[0], str) else metrics
         evalMetrics = self.getConfig("eval.metrics", metrics)
         labelNames = self.getConfig("classification.labelNames")
 

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases/phases/Predict.py

@@ -28,21 +28,6 @@ class Predict(Phase):
     
     CHANNEL_MAPPING_FILE = "lastchannelmapping.json"
     
-    def getModel(self, weightsPath: Optional[str] = None) -> Model:
-        """Load the model with optional custom weights."""
-        if weightsPath:
-            # Load custom weights from specified path
-            model = ModelManager.getModel(True)
-            model.build()
-            model.load(weightsPath)
-        else:
-            # Use default trained model state
-            modelState = self.project.getData("modelState", Model, generate=False)
-            model = ModelManager.getModel(True)
-            model.build()
-            model.loadState(modelState)
-        return model
-    
     def loadChannelMapping(self) -> Dict[str, str]:
         """Load the last used channel mapping from file."""
         mappingPath = self.getConfig("predict.lastChannelMappingPath", self.CHANNEL_MAPPING_FILE)
@@ -169,6 +154,12 @@ class Predict(Phase):
         return self.predictRecordSignal(recordSignal)
 
     def predictRecordSignal(self, recordSignal, metadata=None, dummyY=None):
+        channelMapping = self.getConfig("predict.channelMapping", None)
+
+        for src, dst in (channelMapping or {}).items():
+            if src in recordSignal.signalNames:
+                recordSignal.renameSignal(src, dst)
+
         processedSignal = self.preprocessSignal(recordSignal)
 
         with self.project:
@@ -185,7 +176,10 @@ class Predict(Phase):
 
             # Load model with optional custom weights
             weightsPath = self.getConfig("predict.weights", False)
-            model = self.getModel(weightsPath)
+            if weightsPath:
+                self.setConfig("pretraining.pretrainedModel", weightsPath)
+
+            model = self.project.generateData("trainedModel")
 
             # Run prediction
             prediction = model.predict(processedSignal, returnNumpy=False)

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases/phases/Setup.py

@@ -95,7 +95,7 @@ class Setup(Phase):
             for splitName in ["training", "validation", "test"]:
                 if splitName in foldConfig:
                     dm.addSplitBySlices(splitName, foldConfig[splitName])
-            dm.validatDatasetVersion(raiseException=self.getConfig("validatDataset", True))
+            dm.validateDatasetVersion(raiseException=self.getConfig("validateDataset", True))
             return dm
 
         # add manual addes splits
@@ -136,7 +136,7 @@ class Setup(Phase):
         if "training" not in dm.splits:
             dm.addSplitByRemaining("training", 1)
 
-        dm.validatDatasetVersion(raiseException=self.getConfig("validatDataset", True))
+        dm.validateDatasetVersion(raiseException=self.getConfig("validateDataset", True))
 
         return dm
     

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/SleePyPhases.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SleePyPhases
-Version: 0.8.2
+Version: 0.8.4
 Summary: A framwork for creating deep learning pipelines for sleep data
 Home-page: https://gitlab.com/sleep-is-all-you-need/sleepyphases
 Author: Franz Ehrlich

{sleepyphases-0.8.2 → sleepyphases-0.8.4}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="SleePyPhases",
-    version="v0.8.2"[1:],
+    version="v0.8.4"[1:],
     author="Franz Ehrlich",
     author_email="fehrlichd@gmail.com",
     description="A framwork for creating deep learning pipelines for sleep data",