Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -17,7 +17,7 @@ import torch
 
 _DESCRIPTION = """\
 Dataset for mimic4 data, by default for the Mortality task.
-Available tasks are: Mortality, Length of Stay, Readmission, Phenotype, Mortality Custom, Length of Stay Custom, Readmission Custom, Phenotype Custom.
+Available tasks are: Mortality, Length of Stay, Readmission, Phenotype.
 The data is extracted from the mimic4 database using this pipeline: 'https://github.com/healthylaife/MIMIC-IV-Data-Pipeline/tree/main'
 mimic path should have this form : "path/to/mimic4data/from/username/mimiciv/2.2"
 If you choose a Custom task provide a configuration file for the Time series.
@@ -39,8 +39,6 @@ _CONFIG_URLS = {'los' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/re
 def check_config(task,config_file):
     with open(config_file) as f:
         config = yaml.safe_load(f)
-    if 'Custom' in task:
-        task = task.rsplit('_', 1)[0]
 
     if task=='Phenotype':
         disease_label =  config['disease_label']
@@ -627,37 +625,16 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             version=VERSION,
             description="Dataset for mimic4 Mortality task"
         ),
-        Mimic4DatasetConfig(
-            name="Phenotype Custom",
-            version=VERSION,
-            description="Dataset for mimic4 Custom Phenotype task"
-        ),
-        Mimic4DatasetConfig(
-            name="Readmission Custom",
-            version=VERSION,
-            description="Dataset for mimic4 Custom Readmission task"
-        ),
-        Mimic4DatasetConfig(
-            name="Length of Stay Custom",
-            version=VERSION,
-            description="Dataset for mimic4 Custom Length of Stay task"
-        ),
-        Mimic4DatasetConfig(
-            name="Mortality Custom",
-            version=VERSION,
-            description="Dataset for mimic4 Custom Mortality task"
-        ),
     ]
     
     DEFAULT_CONFIG_NAME = "Mortality"
         
     def create_cohort(self):
-        if self.config.name == 'Phenotype' : self.config_path = _CONFIG_URLS['phenotype'] 
-        if self.config.name == 'Readmission' : self.config_path = _CONFIG_URLS['readmission'] 
-        if self.config.name == 'Length of Stay' : self.config_path = _CONFIG_URLS['los'] 
-        if self.config.name == 'Mortality' : self.config_path = _CONFIG_URLS['mortality']
-        if self.config.name in ['Phenotype Custom','Readmission Custom','Length of Stay Custom','Mortality Custom'] and self.config.name==None:
-            raise ValueError('Please provide a config file')
+        if self.config.name==None:
+            if self.config.name == 'Phenotype' : self.config_path = _CONFIG_URLS['phenotype'] 
+            if self.config.name == 'Readmission' : self.config_path = _CONFIG_URLS['readmission'] 
+            if self.config.name == 'Length of Stay' : self.config_path = _CONFIG_URLS['los'] 
+            if self.config.name == 'Mortality' : self.config_path = _CONFIG_URLS['mortality']
         
         version = self.mimic_path.split('/')[-1]
         mimic_folder= self.mimic_path.split('/')[-2]
@@ -991,8 +968,6 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         with open(filepath, 'rb') as fp:
             dico = pickle.load(fp)
         task=self.config.name.replace(" ","_")
-        #if 'Custom' in task:
-        #    task = task.rsplit('_', 1)[0]
         for key, data in dico.items():
             stat, demo, meds, chart, out, proc, lab, y = getXY_deep(data, task, self.feat_cond,  self.feat_proc,  self.feat_out,  self.feat_chart, self.feat_meds)
             yield int(key), {