diff --git a/README.rst b/README.rst index 0224a25..f92265e 100644 --- a/README.rst +++ b/README.rst @@ -392,6 +392,18 @@ The command outputs the density files in the output-dir and a metadata json file // ... } +Compute MET-types densities update +------------------------------------------------- + +An update to the probabilistic map allows to estimate Morphological and Electrical type densities of inhibitory +and excitatory neurons in the whole brain using `Verasztó et al. (202X)`_'s pipeline. +This pipeline produces transcriptomic types (t-types) densities and a mapping from T-types to canonical neuronal +ME-types as defined in the paper. + +.. code-block:: bash + + sbatch atlas_densities/app/process_t_types_job.sh + Subdivide excitatory files into pyramidal subtypes -------------------------------------------------- diff --git a/atlas_densities/app/convert_t_type_nrrds_to_me_type_nrrds.py b/atlas_densities/app/convert_t_type_nrrds_to_me_type_nrrds.py new file mode 100644 index 0000000..b2bd797 --- /dev/null +++ b/atlas_densities/app/convert_t_type_nrrds_to_me_type_nrrds.py @@ -0,0 +1,160 @@ +import argparse +import glob +import os +from concurrent.futures import as_completed, ProcessPoolExecutor +from tqdm import tqdm +import pandas as pd +import nrrd + +# Paths +PATH_TO_T_TYPES_NRRDS = "./t_type_nrrd_example/" +PATH_TO_P_MAP = "./data/mtypes/probability_map/extended_p_me_t.csv" +OUTPUT_PATH = "./met_nrrd_output" + +def load_p_map(path_to_p_map, max_me_types=None): + """ + Load and preprocess the P-map, filtering out invalid T-type and M-type combinations + based on the provided rules: + - T-types containing 'Glut' can only combine with M-types containing 'PC'. + - T-types containing 'Gaba' can only combine with M-types containing 'IN'. + """ + # Load the P-map + p_map = pd.read_csv(path_to_p_map, index_col=0) + print(f"Loaded P-map shape: {p_map.shape}") + + # Fill NaNs with zeros + p_map = p_map.fillna(0) + print(f"Shape after filling NaNs: {p_map.shape}") + + # Apply filtering rules + def is_unvalid_combination(t_type, m_type): + if "Glut" in t_type and "IN" in m_type: + return True + if "Gaba" in t_type and "PC" in m_type: + return True + return False + + # Filter out invalid combinations + for col in p_map.columns: + for t_type in p_map.index: + if is_unvalid_combination(t_type, col): + p_map.at[t_type, col] = 0.0 + + # Normalize rows + row_sums = p_map.sum(axis=1) + print(f"Row sums before normalization: {row_sums.describe()}") + p_map = p_map.div(row_sums, axis=0).fillna(0) # Normalize and handle NaNs + print(f"Shape after normalization: {p_map.shape}") + + # Create MET keys + stacked_p_map = p_map.stack() + print(f"Stacked P-map shape: {stacked_p_map.shape}") + met_types = [f"{me_type}|{t_type}" for t_type, me_type in stacked_p_map.index] + met_df = pd.DataFrame([stacked_p_map.values], columns=met_types) + print(f"Initial MET DataFrame shape: {met_df.shape}") + + # Filter out MET columns with zero values + met_df = met_df.loc[:, (met_df != 0).any(axis=0)] + print(f"Filtered MET DataFrame shape: {met_df.shape}") + + return met_df + +def setup_output_path(output_path): + """Create output directory if it doesn't exist.""" + if not os.path.exists(output_path): + os.makedirs(output_path) + +def process_met_type(met_type, met_data, t_type_paths, sizes): + """Compute NRRD data for a single MET-type.""" + try: + t_type = met_type.split("|")[2].replace("-","_") # Extract T-type from MET-type + # Check if T-type exists in t_type_paths + if t_type not in t_type_paths: + print(f"Skipping MET-type {met_type}: T-type {t_type} not found in t_type_paths.") + return None + t_type_data, _ = nrrd.read(t_type_paths[t_type]) + if t_type_data.shape != tuple(sizes): + raise ValueError(f"Incorrect dimensions for {t_type}: {t_type_data.shape}") + return t_type_data * met_data.values + except Exception as e: + print(f"Error processing MET-type {met_type}: {e}") + return None + +def save_met_type_result(met_type, data, output_path): + """Save NRRD file for a single MET-type.""" + try: + file_path = os.path.join(output_path, f"{met_type}.nrrd") + nrrd.write(file_path, data) + except Exception as e: + print(f"Error saving MET-type {met_type}: {e}") + +def process_batch(met_types_batch, p_map_subset, t_type_paths, output_path, sizes): + """Process a batch of MET-types.""" + + for met_type in tqdm(met_types_batch, desc="Processing MET-types"): + try: + data = process_met_type(met_type, p_map_subset[met_type], t_type_paths, sizes) + if data is not None: + save_met_type_result(met_type, data, output_path) + except Exception as e: + print(f"Error processing batch for {met_type}: {e}") + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("--start", type=int, required=True, help="Start index of T-types") + parser.add_argument("--end", type=int, required=True, help="End index of T-types") + parser.add_argument( + "--workers", type=int, default=1, help="Number of worker processes to use" + ) + args = parser.parse_args() + + print(f"Processing T-types from index {args.start} to {args.end}...") + + # Ensure indices are valid + t_type_files = sorted(glob.glob(f"{PATH_TO_T_TYPES_NRRDS}/*.nrrd")) + if args.start < 0 or args.end >= len(t_type_files): + raise ValueError(f"Invalid range: {args.start} to {args.end}") + + t_type_batch = t_type_files[args.start:args.end + 1] + print(f"Loaded {len(t_type_batch)} T-types for processing.") + t_type_batch_list = [f.split("/")[-1].replace(".nrrd", "") for f in t_type_batch] + + # Load P-map + p_map = load_p_map(PATH_TO_P_MAP) + setup_output_path(OUTPUT_PATH) + + # Load T-type paths + t_type_files = [f for f in os.listdir(PATH_TO_T_TYPES_NRRDS) if f.endswith(".nrrd")] + t_type_list = sorted([f.replace(".nrrd", "") for f in t_type_files]) + t_type_paths = {t_type: os.path.join(PATH_TO_T_TYPES_NRRDS, f"{t_type}.nrrd") for t_type in t_type_list} + + # Get MET-types and filter range + met_types = list(p_map.columns) + print("all met-types :", len(met_types)) + print(t_type_batch_list[:10]) + print(met_types[:10]) + met_types_batch = [met_type for met_type in met_types if met_type.split("|")[2].replace("-","_") in t_type_batch_list] #met_types[args.start:args.end] + print("batch size :", len(met_types_batch)) + if not met_types_batch: + print(f"No MET-types to process in range {args.start}-{args.end}.") + return + + # Get header from a T-type + init_nrrd, header = nrrd.read(t_type_paths[t_type_list[0]]) + + # Process MET-types in parallel + batch_size = max(1, len(met_types_batch) // args.workers) + with ProcessPoolExecutor(max_workers=args.workers) as executor: + futures = [] + for i in range(0, len(met_types_batch), batch_size): + batch = met_types_batch[i:i + batch_size] + futures.append(executor.submit(process_batch, batch, p_map, t_type_paths, OUTPUT_PATH, header["sizes"])) + + for future in as_completed(futures): + try: + future.result() + except Exception as e: + print(f"Error in parallel execution: {e}") + +if __name__ == "__main__": + main() diff --git a/atlas_densities/app/data/mtypes/probability_map/extended_p_me_t.csv b/atlas_densities/app/data/mtypes/probability_map/extended_p_me_t.csv new file mode 100644 index 0000000..6ba9650 --- /dev/null +++ b/atlas_densities/app/data/mtypes/probability_map/extended_p_me_t.csv @@ -0,0 +1,5169 @@ 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+0042_L6_IT_CTX_Glut_2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1.0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +0049_L6_IT_CTX_Glut_4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1.0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +0063_L5_IT_CTX_Glut_4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.2,,,,0.2,,0.2,0.4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +0247_LA-BLA-BMA-PA_Glut_5,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1.0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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diff --git a/atlas_densities/app/process_t_types_job.sh b/atlas_densities/app/process_t_types_job.sh new file mode 100644 index 0000000..a658554 --- /dev/null +++ b/atlas_densities/app/process_t_types_job.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +#SBATCH --account=proj72 # PUT YOUR PROJ HERE +#SBATCH --job-name=prconvert_t_type_nrrds_to_me_type_nrrds # Job name +#SBATCH --array=0-659 # Job array range (0 to 9 for 10 batches) +#SBATCH --output=./logs/batch_%A_%a.out # Output file +#SBATCH --error=./logs/batch_%A_%a.err # Error file +#SBATCH --time=24:00:00 # Time limit +#SBATCH --mem=0 # Memory per job +#SBATCH --constraint=uc2 +#SBATCH --partition=prod + +# Load Python module +module load unstable +source ../myvenv/bin/activate + +# Define paths +PATH_TO_T_TYPES_NRRDS= #Put your path here : "/gpfs/bbp.cscs.ch/data/project/proj84/csaba/aibs_10x_mouse_wholebrain/results/density_calculations/scaled_nrrd_CCFv3a" +BATCH_SIZE=8 # Maximum number of T-types per job + +# Dynamically calculate total T-types and batch size +TOTAL_T_TYPES=$(ls $PATH_TO_T_TYPES_NRRDS/*.nrrd | wc -l) # Total T-types +NUM_BATCHES=$(( (TOTAL_T_TYPES + BATCH_SIZE - 1) / BATCH_SIZE )) # Total number of batches + +# Validate job array bounds +if [ $SLURM_ARRAY_TASK_ID -ge $NUM_BATCHES ]; then + echo "No T-types to process for task ID $SLURM_ARRAY_TASK_ID." + exit 0 +fi + +# Calculate start and end indices for this job +START=$((SLURM_ARRAY_TASK_ID * BATCH_SIZE)) +END=$((START + BATCH_SIZE - 1)) +if [ $END -ge $TOTAL_T_TYPES ]; then + END=$((TOTAL_T_TYPES - 1)) # Adjust for the last batch +fi + +# Ensure there is at least one T-type to process +if [ $START -gt $END ]; then + echo "No T-types to process for task ID $SLURM_ARRAY_TASK_ID." + exit 0 +fi + +# Run the Python script +echo "Processing T-types from index $START to $END..." +python convert_t_type_nrrds_to_me_type_nrrds.py --start $START --end $END --workers 4 \ No newline at end of file diff --git a/tests/densities/data/test_met_types_data/p_map.csv b/tests/densities/data/test_met_types_data/p_map.csv new file mode 100644 index 0000000..7177d8b --- /dev/null +++ b/tests/densities/data/test_met_types_data/p_map.csv @@ -0,0 +1,4 @@ +,me_type_1,me_type_2,me_type_3 +t_type_1,0.06097936395459393,0.08344702886296308,0.855573607182443 +t_type_2,0.2965659123220969,0.4600813490468502,0.24335273863105283 +t_type_3,0.1511616457634921,0.6198712734707398,0.22896708076576813 diff --git a/tests/densities/data/test_met_types_data/t_type_1.nrrd b/tests/densities/data/test_met_types_data/t_type_1.nrrd new file mode 100644 index 0000000..069917d Binary files /dev/null and b/tests/densities/data/test_met_types_data/t_type_1.nrrd differ diff --git a/tests/densities/test_met_types.py b/tests/densities/test_met_types.py new file mode 100644 index 0000000..1c9a453 --- /dev/null +++ b/tests/densities/test_met_types.py @@ -0,0 +1,82 @@ +import os +import sys +import pytest +import numpy as np +import pandas as pd +import nrrd +from unittest.mock import patch, MagicMock +from pathlib import Path +# # Add parent directory to sys.path +# sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) + +from atlas_densities.app.convert_t_type_nrrds_to_me_type_nrrds import ( + load_p_map, + setup_output_path, + process_t_type, + save_me_type_results, + process_batch, +) + + +# Test load_p_map +def test_load_p_map(): + # Synthetic P-map data + csv_data = """ME_TYPE_1,ME_TYPE_2 +T_TYPE_1,0.4,0.6 +T_TYPE_2,0.3,0.7""" + p_map_path = "test_p_map.csv" + with open(p_map_path, "w") as f: + f.write(csv_data) + + # Test function + p_map = load_p_map(p_map_path) + assert "ME_TYPE_1|T_TYPE_1" in p_map.columns + assert "ME_TYPE_2|T_TYPE_2" in p_map.columns + assert np.isclose(p_map.loc["T_TYPE_1"]["ME_TYPE_1|T_TYPE_1"], 0.4) + + os.remove(p_map_path) + + +# Test setup_output_path +def test_setup_output_path(tmp_path): + output_path = tmp_path / "test_output" + setup_output_path(output_path) + assert os.path.exists(output_path) + + +# Test process_t_type +def test_process_t_type(): + # Mock T-type data + t_type_data = np.ones((10, 10, 10)) + t_type_path = "test_t_type.nrrd" + nrrd.write(t_type_path, t_type_data) + + # Mock P-map subset + p_map_subset = pd.Series({"ME_TYPE_1": 0.4, "ME_TYPE_2": 0.6}) + + # Test function + me_type_results = process_t_type("test_t_type", t_type_path, p_map_subset, (10, 10, 10)) + assert np.allclose(me_type_results["ME_TYPE_1"], t_type_data * 0.4) + assert np.allclose(me_type_results["ME_TYPE_2"], t_type_data * 0.6) + + os.remove(t_type_path) + + +# Test save_me_type_results +def test_save_me_type_results(tmp_path): + output_path = tmp_path / "output" + setup_output_path(output_path) + + # Mock ME-type data + me_type_accum = { + "ME_TYPE_1": np.ones((5, 5, 5)) * 0.4, + "ME_TYPE_2": np.ones((5, 5, 5)) * 0.6, + } + + # Test function + save_me_type_results(me_type_accum, output_path) + for me_type in me_type_accum: + file_path = output_path / f"{me_type}.nrrd" + assert file_path.exists() + data, _ = nrrd.read(file_path) + assert np.allclose(data, me_type_accum[me_type])