SleePyPhases 0.2.1__tar.gz → 0.3.0__tar.gz

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SleePyPhases
-Version: 0.2.1
+Version: 0.3.0
 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-0.2.1 → sleepyphases-0.3.0}/SleePyPhases/MultiScorer.py

@@ -42,19 +42,27 @@ class MultiScorer(Scorer):
             if isinstance(predictions, list) or isinstance(predictions, tuple):
                 p = predictions[i]
             elif predictions.shape[-1] == len(self.multiClassNums):
+                if len(predictions.shape) == 3:
+                    predictions = predictions.reshape(-1, predictions.shape[-1])
                 p = predictions[:, i]
             else:
                 start = sum(self.multiClassNums[:i])
                 end = start + self.multiClassNums[i]
+                if len(predictions.shape) == 3:
+                    predictions = predictions.reshape(-1, predictions.shape[-1])
                 p = predictions[:, start:end]
             
             if isinstance(truth, list) or isinstance(truth, tuple):
                 t = truth[i]
             elif truth.shape[-1] == len(self.multiClassNums):
+                if len(truth.shape) == 3:
+                    truth = truth.reshape(-1, truth.shape[-1])
                 t = truth[:, i]
             else:
                 start = sum(self.multiClassNums[:i])
                 end = start + self.multiClassNums[i]
+                if len(truth.shape) == 3:
+                    truth = truth.reshape(-1, truth.shape[-1])
                 t = truth[:, start:end]
 
             

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/SleePyPhases/phases/Eval.py

@@ -81,7 +81,7 @@ class Eval(Phase):
 
         # setup data and scorer
         
-        classNums = self.getConfig("model.multiclassificationSize", [2])
+        classNums = self.getConfig("numClasses", [2])
         labelNames = self.getConfig("classification.labelNames")
         ignoreIndex = self.getConfig("classification.ignoreIndex", -1)
         metrics = self.getConfig("trainingParameter.validationMetrics")
@@ -99,16 +99,10 @@ class Eval(Phase):
 
         for data in tqdm(testData):
             x, truth = data
-            # make sure to have a batchsize if batchSize == 1
-            x = x.reshape(batchSize, x.shape[0], x.shape[1])
-            truth = truth.reshape(batchSize, truth.shape[0], truth.shape[1])
 
-            prediction = model.predict(x, get_likelihood=True, returnNumpy=False)
+            prediction = model.predict(x, returnNumpy=False)
             prediction, truth = da((prediction, truth))
 
-            # prediction = prediction.reshape(-1, prediction.shape[2])
-            # truth = truth.reshape(-1, truth.shape[2])
-
             scorer.score(truth, prediction, trace=True)
 
         result = scorer.scoreAllRecords()
@@ -152,7 +146,7 @@ class Eval(Phase):
             self.project.config.update(self.getConfig("eventEval", {}))
 
             evalMetrics = self.getConfig("eval.metrics")
-            classNums = self.getConfig("model.multiclassificationSize", [2])
+            classNums = self.getConfig("numClasses", [2])
             labelNames = self.getConfig("classification.labelNames")
             predictionNames = self.getConfig("classification.predictionSignals")
             predictionFrequencies = self.getConfig("classification.predictionFrequencies")
@@ -193,7 +187,7 @@ class Eval(Phase):
                     x = x.reshape([1] + list(x.shape))
                     truth = truth.reshape([1] + list(truth.shape))
 
-                prediction = model.predict(x, get_likelihood=True, returnNumpy=False)
+                prediction = model.predict(x, returnNumpy=False)
                 prediction, truth = da((prediction, truth))
 
                 # for labelIndex, labelName in enumerate(recordResults.keys()):

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/SleePyPhases/phases/EvalReport.py

@@ -10,7 +10,6 @@ from pyPhasesRecordloader import RecordSignal, Signal
 
 from SleePyPhases import Plot
 from SleePyPhases.DataManipulation import DataManipulation
-from SleePyPhases.Reporter import Reporter
 
 
 class EvalReport(Phase):
@@ -244,8 +243,8 @@ class EvalReport(Phase):
     def copyRawData(self):
         modelConfigString = self.project.getDataFromName("modelState").getTagString()
         trainingLogPath = f"logs/{modelConfigString}/"
-        shutil.copyfile(trainingLogPath + "log.csv", Reporter.basePath + "training.log")
-        shutil.copyfile(trainingLogPath + "project.config", Reporter.basePath + "project.json")
+        shutil.copyfile(trainingLogPath + "log.csv", self.evalPath + "training.log")
+        shutil.copyfile(trainingLogPath + "project.config", self.evalPath + "project.json")
 
     def trainingPlot(self, logFile):
         import matplotlib.pyplot as plt

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/SleePyPhases/phases/ExtractFeatures.py

@@ -209,18 +209,15 @@ class ExtractFeatures(Phase):
         self.features = None
         metadata = self.project.getData("metadata", pd.DataFrame)
         recordIds = metadata["recordId"]
+        forceCalculation = self.getConfig("featureExtraction.features", True)
 
         reqFeatures = {f["name"]: True for f in self.getConfig("featureExtraction.features", [])}
 
-        # groupedRecords = {"pid_202436073": "acq_237478592"}
         for recordId in tqdm(recordIds.iloc):
-            # tryToGenerate has no meaning, it is just known to be not in the metadata, so the record will always be recalculated
-            # self.getData("features", pd.DataFrame, recordId=recordId, tryToGenerate=True, **reqFeatures)
+            if forceCalculation:
+                # the parameter forced has no meaning, it is just known to be not in the metadata, so the record will always be recalculated
+                reqFeatures["forced"] = True # should never be found
             rows = self.getData("features", pd.DataFrame, recordId=recordId, **reqFeatures)
             if len(rows) == 0:
                 self.logError(f"no features for {recordId}")
                 
-
-        # get a single feature:
-        # feat = {"swa": True}
-        # x = self.getData("features", pd.DataFrame, recordId="shhs1-200002", channel="EEG", **feat)   

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/SleePyPhases/phases/Setup.py

@@ -4,7 +4,6 @@ from pyPhases import Phase
 from pyPhasesML import DataversionManager, Scorer
 from pyPhasesRecordloader import RecordLoader
 
-from SleePyPhases.recordloaders.MedicalDB import MedicalDB
 
 
 class Setup(Phase):
@@ -17,21 +16,6 @@ class Setup(Phase):
         
         defaultValidationbatchManipulation = self.getConfig("segmentManipulationEval", self.getConfig("segmentManipulation"))
         self.setConfig("segmentManipulationEval", defaultValidationbatchManipulation)
-        
-        # alice loader
-        RecordLoader.registerRecordLoader("RecordLoaderTest", "SleePyPhases.recordloaders")
-        RecordLoader.registerRecordLoader("RecordLoaderTSM", "SleePyPhases.recordloaders")
-        tsmPath = self.getConfig("tsm-path", False)
-        if tsmPath is not False:
-            tsmPath = Path(tsmPath)
-            self.project.setConfig("loader.tsm.filePath", tsmPath.as_posix())
-            self.project.setConfig("loader.tsm.dataset.downloader.basePath", tsmPath.as_posix())
-
-        tsmPath = self.getConfig("tsm-domino-path", False)
-        if tsmPath is not False:
-            tsmPath = Path(tsmPath)
-            self.project.setConfig("loader.tsm-domino.filePath", tsmPath.as_posix())
-            self.project.setConfig("loader.tsm-domino.dataset.downloader.basePath", tsmPath.as_posix())
 
         preprocessingConfig = self.getConfig("preprocessing")
         if "combineChannels" in preprocessingConfig:
@@ -62,9 +46,6 @@ class Setup(Phase):
             return kappa
         Scorer.registerMetric("reduceAndKappa", reduceKappa, combineReduceKappa)
         
-        MedicalDB.config = self.getConfig("medicalDB", {})
-
-            
     def getDataVersionManager(self):
         groupedRecords = self.project.getData("allDBRecordIds", list)
         seed = self.getConfig("dataversion.seed", None)

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/SleePyPhases.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SleePyPhases
-Version: 0.2.1
+Version: 0.3.0
 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-0.2.1 → sleepyphases-0.3.0}/SleePyPhases.egg-info/SOURCES.txt

@@ -40,9 +40,6 @@ SleePyPhases/phases/Training.py
 SleePyPhases/phases/Validation.py
 SleePyPhases/phases/VisualizeConfig.py
 SleePyPhases/phases/__init__.py
-SleePyPhases/recordloaders/MedicalDB.py
-SleePyPhases/recordloaders/RecordLoaderTSM.py
-SleePyPhases/recordloaders/__init__.py
 tests/__init__.py
 tests/conftest.py
 tests/unit/__init__.py

{sleepyphases-0.2.1 → sleepyphases-0.3.0}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="SleePyPhases",
-    version="v0.2.1"[1:],
+    version="v0.3.0"[1:],
     author="Franz Ehrlich",
     author_email="fehrlichd@gmail.com",
     description="A framwork for creating deep learning pipelines for sleep data",

sleepyphases-0.2.1/SleePyPhases/recordloaders/MedicalDB.py

@@ -1,124 +0,0 @@
-import sys
-
-from pyPhases.util.Logger import classLogger
-from pypika import Table, PostgreSQLQuery as Query
-from pypika.queries import QueryBuilder
-
-
-@classLogger
-class MedicalDB:
-    connection = None
-    client = None
-    assocCursor = None
-    _instance = None
-
-    config = {
-        "user": "root",
-        "password": "example",
-        "host": "localhost",
-        "port": 5432,
-        "database": "data",
-    }
-
-    @classmethod
-    def get(cls) -> "MedicalDB":
-        if cls._instance is None:
-            cls._instance = cls.__new__(cls)
-            cls._instance.connect()
-        return cls._instance
-
-    def connect(self):
-
-        import psycopg2
-
-        try:
-            c = MedicalDB.config
-            conn = psycopg2.connect(
-                "host=%s port=%i dbname=%s user=%s password=%s"
-                % (
-                    c["host"],
-                    c["port"],
-                    c["database"],
-                    c["user"],
-                    c["password"],
-                )
-            )
-
-        except psycopg2.Error as e:
-            self.logError(f"Error connecting to Postgres Platform: {e}")
-            sys.exit(1)
-        self.conn = conn
-        self.cursor = conn.cursor()
-
-    def execute(self, sql, **vars):
-        if isinstance(sql, QueryBuilder):
-            sql = sql.get_sql()
-        return self.cursor.execute(sql, **vars)
-
-    def executeAndFetch(self, sql, **vars):
-        self.execute(sql, **vars)
-        return self.cursor.fetchall()
-
-    def commit(self):
-        self.conn.commit()
-    
-    def executeAndFetchOne(self, sql, **vars):
-        self.execute(sql, **vars)
-        return self.cursor.fetchone()
-
-    def close(self):
-        if self.connection is not None:
-            self.connection.close()
-
-    def fillRecordId(self, id):
-        return id
-
-    def getRecordData(self, recordId):
-        record = Table("record", schema=self.config["schema"])
-        patient = Table("patient", schema=self.config["schema"])
-        medCase = Table("medical_case", schema=self.config["schema"])
-        q = (
-            Query.from_(record)
-            .select(patient.id_patient, record.id_medical_case, record.start, patient.date_of_birth, patient.gender)
-            .join(medCase).on(record.id_medical_case == medCase.id_medical_case)
-            .join(patient).on(patient.id_patient == medCase.id_patient)
-            .where(record.id_record == recordId)
-        )
-        row = self.executeAndFetchOne(q)
-
-        if row is None:
-            return None
-        
-        row = list(row)
-        age = None if row[2] or row[3] is None else row[2] - row[3]
-        row[3] = age
-
-        return row
-
-    def getDiagnoses(self, recordId):
-        diag = Table("diagnosis", schema=self.config["schema"])
-        record = Table("record", schema=self.config["schema"])
-        medCase = Table("medical_case", schema=self.config["schema"])
-        q = Query.from_(diag)\
-            .select("diagnosis_category_id", "diagnosis")\
-            .join(medCase).on(diag.id_medical_case == medCase.id_medical_case)\
-            .join(record).on(medCase.id_medical_case == record.id_medical_case)\
-            .where(record.id_record == recordId)\
-            .get_sql()
-        
-        diagnoses = self.executeAndFetch(q)
-
-        diagnoseCats = {d[0]: d[1] for d in diagnoses}
-        return diagnoseCats
-
-    def getPSGType(self, recordId):
-
-        record = Table("record", schema=self.config["schema"])
-        q = (
-            Query.from_(record)
-            .select("psg_config")
-            .where(record.id_record == recordId)
-        )
-        r = self.executeAndFetchOne(q)
-
-        return r[0] if bool(r) else ""

sleepyphases-0.2.1/SleePyPhases/recordloaders/RecordLoaderTSM.py

@@ -1,34 +0,0 @@
-from SleePyPhases.recordloaders.MedicalDB import MedicalDB
-from SleepHarmonizer import RecordLoaderAlice
-
-
-class RecordLoaderTSM(RecordLoaderAlice):
-    config = {}
-
-    def getMetaData(self, recordName):
-        metadata = super().getMetaData(recordName)
-        del metadata["patientName"]
-        del metadata["patientCode"]
-        del metadata["patientAdd"]
-        del metadata["technician"]
-
-        db = MedicalDB.get()
-        row = db.getRecordData(recordName)
-        diagnoses = db.getDiagnoses(recordName)
-        metadata["psg_type"] = db.getPSGType(recordName)
-
-        if row is not None:
-            patient_id, case_id, recordDate, patientAge, gender = row
-
-            metadata["patient"] = patient_id
-            metadata["case"] = case_id
-            metadata["age"] = patientAge
-            metadata["gender"] = gender
-            metadata["startRecord"] = recordDate
-
-        if diagnoses is not None:
-            metadata.update(diagnoses)
-        
-        db.close()
-
-        return metadata