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+{
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+ "cells": [
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+ {
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+ "cell_type": "code",
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+ "execution_count": 9,
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "Processing session1...\n",
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+ " Adding Trial 1...\n",
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+ " Adding Trial 2...\n",
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+ "Processing session2...\n",
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+ " Adding Trial 3...\n",
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+ " Adding Trial 4...\n",
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+ "NIX file created and annotated with metadata.\n"
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+ ]
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+ }
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+ ],
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+ "source": [
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+ "# Import necessary libraries\n",
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+ "import pandas as pd\n",
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+ "import nixio as nix\n",
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+ "import numpy as np\n",
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+ "\n",
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+ "# ---------------------------\n",
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+ "# Part 1: Read CSV Files\n",
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+ "# ---------------------------\n",
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+ "\n",
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+ "# Read the metadata CSV file\n",
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+ "metadata_df = pd.read_csv('metadata.csv')\n",
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+ "\n",
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+ "# Read spike times CSV files for each session\n",
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+ "session_files = ['session1_spikes.csv', 'session2_spikes.csv']\n",
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+ "spike_dfs = {}\n",
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+ "\n",
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+ "for session_file in session_files:\n",
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+ " session_id = session_file.split('_')[0] # Extract session ID from file name\n",
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+ " spike_dfs[session_id] = pd.read_csv(session_file)\n",
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+ "\n",
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+ "# ---------------------------\n",
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+ "# Part 2: Create NIX File\n",
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+ "# ---------------------------\n",
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+ "\n",
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+ "# Create a new NIX file\n",
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+ "nix_file = nix.File.open('neural_data.nix', nix.FileMode.Overwrite)\n",
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+ "\n",
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+ "# ---------------------------\n",
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+ "# Part 3: Add Data to NIX File\n",
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+ "# ---------------------------\n",
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+ "\n",
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+ "# Iterate over sessions\n",
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+ "for session_id, spike_df in spike_dfs.items():\n",
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+ " print(f'Processing {session_id}...')\n",
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+ "\n",
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+ " # Create a block for the session\n",
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+ " block = nix_file.create_block(f'Session {session_id}', 'nix.session')\n",
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+ " \n",
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+ " # Get trials for this session\n",
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+ " session_trials = metadata_df[metadata_df['session_id'] == session_id]\n",
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+ " \n",
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+ " # Iterate over trials\n",
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+ " for index, trial in session_trials.iterrows():\n",
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+ " trial_id = trial['trial_id']\n",
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+ " print(f' Adding Trial {trial_id}...')\n",
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+ " \n",
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+ " # Create a group for the trial\n",
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+ " trial_group = block.create_group(f'Trial {int(trial_id)}', 'nix.trial')\n",
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+ " \n",
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+ " # Get spike times for this trial\n",
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+ " trial_spikes = spike_df[spike_df['trial_id'] == trial_id]\n",
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+ " \n",
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+ " # Group spike times by unit_id (channel)\n",
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+ " units = trial_spikes['unit_id'].unique()\n",
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+ " \n",
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+ " for unit in units:\n",
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+ " # Get spike times for the unit\n",
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+ " unit_spike_times = trial_spikes[trial_spikes['unit_id'] == unit]['spike_time'].values\n",
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+ " \n",
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+ " # Create a data array for the spike times with a unique name\n",
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+ " data_array = block.create_data_array(f'Trial {int(trial_id)} Unit {int(unit)} Spike Times', 'nix.data.spike_times', data=unit_spike_times)\n",
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+ " data_array.unit = 's' # Set the unit of the data\n",
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+ " data_array.label = f'Unit {int(unit)}' # Set the label for the data array\n",
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+ " \n",
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+ " # Add the data array to the trial group\n",
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+ " trial_group.data_arrays.append(data_array)\n",
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+ " \n",
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+ " # Add trial metadata to the trial group\n",
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+ " trial_metadata = nix_file.create_section(f'Trial {int(trial_id)} Metadata', 'nix.metadata.trial')\n",
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+ " trial_metadata['start_time'] = trial['start_time']\n",
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+ " trial_metadata['end_time'] = trial['end_time']\n",
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+ " trial_metadata['target_1'] = [trial['target_1_x'], trial['target_1_y']]\n",
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+ " trial_metadata['target_2'] = [trial['target_2_x'], trial['target_2_y']]\n",
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+ " trial_metadata['reward_value'] = trial['reward_value']\n",
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+ " \n",
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+ " # Link metadata to the trial group\n",
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+ " trial_group.metadata = trial_metadata\n",
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+ "\n",
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+ "# ---------------------------\n",
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+ "# Part 4: Close NIX File\n",
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+ "# ---------------------------\n",
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+ "\n",
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+ "# Close the NIX file\n",
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+ "nix_file.close()\n",
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+ "\n",
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+ "print('NIX file created and annotated with metadata.')\n"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "## Exploring the NIX File\n",
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+ "\n",
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+ "After creating the NIX file, you can explore it using NIXIO or other tools that support the NIX format, such as for GUI experience, [HDF5 viewer](https://www.hdfgroup.org/downloads/hdfview/)."
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 10,
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "Block: Session session1\n",
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+ " Group: Trial 1\n",
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+ " DataArray: Trial 1 Unit 1 Spike Times, Label: Unit 1, Unit: s\n",
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+ " DataArray: Trial 1 Unit 2 Spike Times, Label: Unit 2, Unit: s\n",
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+ " Metadata for Trial 1:\n",
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+ " start_time: (0.0,)\n",
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+ " end_time: (10.0,)\n",
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+ " target_1: (5.0, 5.0)\n",
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+ " target_2: (-5.0, 5.0)\n",
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+ " reward_value: (10,)\n",
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+ " Group: Trial 2\n",
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+ " DataArray: Trial 2 Unit 1 Spike Times, Label: Unit 1, Unit: s\n",
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+ " DataArray: Trial 2 Unit 2 Spike Times, Label: Unit 2, Unit: s\n",
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+ " Metadata for Trial 2:\n",
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+ " start_time: (11.0,)\n",
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+ " end_time: (21.0,)\n",
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+ " target_1: (5.0, 5.0)\n",
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+ " target_2: (-5.0, 5.0)\n",
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+ " reward_value: (5,)\n",
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+ "Block: Session session2\n",
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+ " Group: Trial 3\n",
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+ " DataArray: Trial 3 Unit 1 Spike Times, Label: Unit 1, Unit: s\n",
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+ " DataArray: Trial 3 Unit 2 Spike Times, Label: Unit 2, Unit: s\n",
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+ " Metadata for Trial 3:\n",
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+ " start_time: (0.0,)\n",
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+ " end_time: (9.5,)\n",
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+ " target_1: (5.0, 5.0)\n",
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+ " target_2: (-5.0, 5.0)\n",
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+ " reward_value: (15,)\n",
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+ " Group: Trial 4\n",
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+ " DataArray: Trial 4 Unit 1 Spike Times, Label: Unit 1, Unit: s\n",
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+ " DataArray: Trial 4 Unit 2 Spike Times, Label: Unit 2, Unit: s\n",
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+ " Metadata for Trial 4:\n",
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+ " start_time: (10.0,)\n",
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+ " end_time: (20.0,)\n",
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+ " target_1: (5.0, 5.0)\n",
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+ " target_2: (-5.0, 5.0)\n",
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+ " reward_value: (10,)\n"
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+ ]
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+ }
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+ ],
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+ "source": [
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+ "# Open the NIX file\n",
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+ "nix_file = nix.File.open('neural_data.nix', nix.FileMode.ReadOnly)\n",
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+ "\n",
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+ "# List all blocks (sessions)\n",
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+ "for block in nix_file.blocks:\n",
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+ " print(f'Block: {block.name}')\n",
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+ " \n",
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+ " # List all groups (trials) in the block\n",
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+ " for group in block.groups:\n",
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+ " print(f' Group: {group.name}')\n",
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+ " \n",
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+ " # List all data arrays (units) in the group\n",
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+ " for da in group.data_arrays:\n",
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+ " print(f' DataArray: {da.name}, Label: {da.label}, Unit: {da.unit}')\n",
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+ " \n",
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+ " # Access metadata\n",
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+ " if group.metadata:\n",
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+ " print(f' Metadata for {group.name}:')\n",
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+ " for prop in group.metadata.props:\n",
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+ " print(f' {prop.name}: {prop.values}')\n",
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+ " \n",
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+ "# Close the NIX file\n",
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+ "nix_file.close()\n"
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+ ]
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+ }
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+ ],
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+ "metadata": {
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+ "kernelspec": {
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+ "display_name": "andani-dataset4",
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+ "language": "python",
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+ "name": "python3"
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+ },
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+ "language_info": {
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+ "codemirror_mode": {
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+ "name": "ipython",
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+ "version": 3
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+ },
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+ "file_extension": ".py",
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+ "mimetype": "text/x-python",
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+ "name": "python",
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+ "nbconvert_exporter": "python",
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+ "pygments_lexer": "ipython3",
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+ "version": "3.13.0"
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+ }
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+ },
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+ "nbformat": 4,
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+ "nbformat_minor": 2
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+}
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