pushing group plot logic, not yet tailored for vosslab linux

Author: miloswrath

code/main.py

@@ -1,23 +1,24 @@
 from utils.mnt import create_symlinks
 from utils.save import Save
+from utils.group import Group
 from core.gg import GG
 import sys
 
-INT_DIR = '/mnt/nfs/lss/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test'
-OBS_DIR = '/mnt/nfs/lss/vosslabhpc/Projects/BOOST/ObservationalStudy/3-experiment/data/act-obs-test'
-RDSS_DIR = '/mnt/nfs/rdss/vosslab/Repositories/Accelerometer_Data'
 
-class pipe:
+class Pipe:
+    INT_DIR = '/mnt/nfs/lss/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test'
+    OBS_DIR = '/mnt/nfs/lss/vosslabhpc/Projects/BOOST/ObservationalStudy/3-experiment/data/act-obs-test'
+    RDSS_DIR = '/mnt/nfs/rdss/vosslab/Repositories/Accelerometer_Data'
     def __init__(self, token, daysago):
         self.token = token
         self.daysago = daysago
 
     def run_pipe(self):
         self._create_syms()
         matched = Save(
-            intdir=INT_DIR,
-            obsdir=OBS_DIR,
-            rdssdir=RDSS_DIR,
+            intdir=self.INT_DIR,
+            obsdir=self.OBS_DIR,
+            rdssdir=self.RDSS_DIR,
             token=self.token,
             daysago=self.daysago
         ).save()
@@ -26,7 +27,10 @@ def run_pipe(self):
             file.write('{\n}')
             file.write(',\n'.join(f'   "{key}": "{value}"' for key, value in matched.items()))
 
-        GG(matched=matched, intdir=INT_DIR, obsdir=OBS_DIR).run_gg()
+        GG(matched=matched, intdir=self.INT_DIR, obsdir=self.OBS_DIR).run_gg()
+        Group().plot_person()
+        Group().plot_session()
+
         return None
 
     def _create_syms(self):
@@ -53,5 +57,5 @@ def _create_syms(self):
         print("Error: <token> cannot be empty.")
         sys.exit(1)
 
-    p = pipe(token, daysago)
+    p = Pipe(token, daysago)
     p.run_pipe()

code/utils/group.py

@@ -2,6 +2,7 @@
 import pandas as pd
 import plotly.graph_objects as go
 import logging
+from main import Pipe 
 
 # Set up logging
 logging.basicConfig(level=logging.INFO)
@@ -10,11 +11,12 @@
 
 class Group:
     def __init__(self):
-        self.obs_path = "/Volumes/vosslabhpc/Projects/BOOST/ObservationalStudy/3-experiment/data/act-obs-test/derivatives/GGIR-3.2.6-test"
-        self.int_path = "/Volumes/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test/derivatives/GGIR-3.2.6-test"
+        self.obs_path = Pipe.OBS_DIR 
+        self.int_path = Pipe.INT_DIR
         self.paths = [self.obs_path, self.int_path]
         self.path = './plots/group'
 
+
     def _parse_person_file(self, file_path):
         try:
             df = pd.read_csv(file_path)

code/utils/qc.py

@@ -1,5 +1,6 @@
 import os
 import pandas as pd
+from main import Pipe
 from utils.plots import ACT_PLOTS, create_json
 
 
@@ -26,16 +27,11 @@ def __init__(self, project: str):
 
         # Determine the expected days worn based on project type
         if project == 'obs':
-            self.base_dir = ( "/Volumes/vosslabhpc/Projects/BOOST/ObservationalStudy/"
-                "3-experiment/data/act-obs-test/derivatives/GGIR-3.2.6-test"
-            )
+            self.base_dir = (Pipe.OBS_DIR)
             self.n_days_worn = 7
         elif project == 'int':
             self.n_days_worn = 9
-            self.base_dir = (
-                "/Volumes/vosslabhpc/Projects/BOOST/InterventionStudy/"
-                "3-experiment/data/act-int-test/derivatives/GGIR-3.2.6-test"
-            )
+            self.base_dir = (Pipe.INT_DIR)
         else:
             raise ValueError("Project must be 'obs' or 'int'")
 

cron.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Source the Conda activate script
+source /opt/anaconda3-2024.10-1/etc/profile.d/conda.sh
+
+# Activate Conda env
+conda activate act
+
+# Move to project home dir
+cd "$(dirname "$0")"
+
+# run pipe
+cd code && python main.py 1