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Add Measurement Fix and Export Options #328

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Add Measurement Fix and Export Options #328

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f622b35
fix rfid sending blank data
jackbelyeu May 5, 2025
013c050
filter measurements used for inital sorting
jackbelyeu May 5, 2025
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13 changes: 5 additions & 8 deletions databases/experiment_database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,9 +79,9 @@ def setup_groups(self, group_names, cage_capacity):
def add_measurement(self, animal_id, value):
'''Adds a new measurement for an animal.'''
timestamp = datetime.now()
self._c.execute('''INSERT INTO animal_measurements (animal_id, timestamp, value)
VALUES (?, ?, ?)''',
(animal_id, timestamp, value))
self._c.execute('''INSERT INTO animal_measurements (animal_id, timestamp, value, measurement_id)
VALUES (?, ?, ?,?)''',
(animal_id, timestamp, value, 1))
self._conn.commit()

def get_measurements_by_date(self, date):
Expand Down Expand Up @@ -502,7 +502,7 @@ def export_to_single_formatted_csv(self, directory):
experiment_df = pd.read_sql_query("SELECT * FROM experiment", self._conn)
animals_df = pd.read_sql_query("SELECT * FROM animals", self._conn)
groups_df = pd.read_sql_query("SELECT * FROM groups", self._conn)
measurements_df = pd.read_sql_query("SELECT * FROM animal_measurements", self._conn)
measurements_df = pd.read_sql_query("SELECT * FROM animal_measurements WHERE measurement_id IS NOT 0", self._conn)

# Add fixed metadata (like measurement name) to experiment table if needed
experiment_df["measurement"] = "Weight" # or fetch from DB if stored
Expand All @@ -511,9 +511,6 @@ def export_to_single_formatted_csv(self, directory):
merged_df = measurements_df.merge(animals_df, on="animal_id", how="left")
merged_df = merged_df.merge(groups_df, on="group_id", how="left")

# Ensure timestamp is datetime
merged_df["timestamp"] = pd.to_datetime(merged_df["timestamp"])

# Pivot the data
pivot_df = merged_df.pivot_table(
index=["name", "animal_id"], # group name and animal id
Expand All @@ -540,7 +537,7 @@ def export_to_single_formatted_csv(self, directory):


def export_to_csv(self, directory):
'''Exports all relevant tables in the database to a folder named after the experiment in the specified directory.'''
'''Exports the full database for testing purposes. Exports each table as a separate file to a folder in the specified directory.'''
import pandas as pd

# Get the experiment name
Expand Down
2 changes: 1 addition & 1 deletion experiment_pages/experiment/data_collection_ui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -496,7 +496,7 @@ def check_for_data():
current_index = self.animal_ids.index(animal_id)

while current_index < len(self.animal_ids) and self.thread_running:
if len(data_handler.received_data) >= 2: # Customize condition
if len(data_handler.received_data) >= 2 and data_handler.received_data != " " and data_handler.received_data is not None and data_handler.received_data != 0:
received_data = data_handler.get_stored_data()
entry.insert(1, received_data)
data_handler.stop()
Expand Down