mirror of
https://gitea.psi.ch/APOG/acsmnode.git
synced 2025-06-24 21:21:08 +02:00
Refactor steps using main functions from each step instead of subprocess with command line interface
This commit is contained in:
@ -2,28 +2,9 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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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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"c:\\Users\\florez_j\\Documents\\GitLab\\acsmnode\\dima\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\python310.zip\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\DLLs\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\lib\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\n",
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"\n",
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"C:\\Users\\florez_j\\AppData\\Roaming\\Python\\Python310\\site-packages\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\lib\\site-packages\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\lib\\site-packages\\win32\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\lib\\site-packages\\win32\\lib\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\lib\\site-packages\\Pythonwin\n",
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"c:\\ProgramData\\Anaconda3\\envs\\flaggingapp_env\\lib\\site-packages\\setuptools\\_vendor\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"import sys\n",
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"import os\n",
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@ -31,11 +12,11 @@
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"\n",
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"\n",
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"notebook_dir = os.getcwd() # Current working directory (assumes running from notebooks/)\n",
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"#project_path = os.path.normpath(os.path.join(notebook_dir, \"..\")) # Move up to project root\n",
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"dima_path = os.path.normpath(os.path.join(notebook_dir, \"dima\")) # Move up to project root\n",
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"project_path = os.path.normpath(os.path.join(notebook_dir, \"..\")) # Move up to project root\n",
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"dima_path = os.path.normpath(os.path.join(project_path, \"dima\")) # Move up to project root\n",
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"\n",
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"#if project_path not in sys.path: # Avoid duplicate entries\n",
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"# sys.path.append(project_path)\n",
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"if project_path not in sys.path: # Avoid duplicate entries\n",
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" sys.path.append(project_path)\n",
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"if dima_path not in sys.path:\n",
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" sys.path.insert(0,dima_path)\n",
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"#sys.path.append(os.path.join(root_dir,'dima','instruments'))\n",
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@ -48,7 +29,9 @@
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"\n",
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"\n",
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"for item in sys.path:\n",
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" print(item)\n"
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" print(item)\n",
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"\n",
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"CAMPAIGN_DATA_FILE = \"../data/collection_JFJ_2024_2025-03-17_2025-02-17.h5\""
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]
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},
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{
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@ -58,60 +41,20 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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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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"File path: c:\\Users\\florez_j\\Documents\\GitLab\\acsmnode\\pipelines\\steps\\apply_calibration_factors.py\n",
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"data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10.h5\n",
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" dataset_name ... parent_file\n",
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"0 ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt/data_... ... ACSM_JFJ_2024_meta.txt\n",
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"1 ACSM_TOFWARE/2024/ACSM_JFJ_2024_timeseries.txt... ... ACSM_JFJ_2024_timeseries.txt\n",
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"2 ACSM_TOFWARE/2024/Org_data_valid.csv/data_table ... Org_data_valid.csv\n",
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"3 ACSM_TOFWARE/2024/Org_err_valid.csv/data_table ... Org_err_valid.csv\n",
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"4 ACSM_TOFWARE/2024/Org_mz_valid.csv/data_table ... Org_mz_valid.csv\n",
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"\n",
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"[5 rows x 3 columns]\n",
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"ACSM_JFJ_2024_timeseries.txt\n",
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"pipelines/params/calibration_factors.yaml\n",
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"Path to output directory : data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10\n",
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"Processing script : pipelines\\steps\\apply_calibration_factors.py\n",
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"Output directory : data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_processed/2024\n",
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"NO3_11000\n",
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"SO4_11000\n",
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"NH4_11000\n",
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"Org_11000\n",
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"Chl_11000\n",
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"Org_44_11000\n",
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"Org_43_11000\n",
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"Org_60_11000\n",
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"NO3_30_11000\n",
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"SO4_98_11000\n",
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"SO4_81_11000\n",
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"SO4_82_11000\n",
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"SO4_62_11000\n",
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"SO4_48_11000\n",
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"Metadata for calibrated data saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_processed/2024/data_lineage_metadata.json\n",
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"Metadata for calibrated data saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_processed/2024/data_lineage_metadata.json\n",
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"Calibration factors saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_processed/2024/ACSM_JFJ_2024_timeseries_calibration_factors.csv\n",
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"Calibrated data saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_processed/2024/ACSM_JFJ_2024_timeseries_calibrated.csv\n",
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"Data lineage saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10\n",
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"\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"from pipelines.steps.apply_calibration_factors import main as run_apply_calibration_factors\n",
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"\n",
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"path_to_data_file = 'data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10.h5'\n",
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"path_to_data_file = CAMPAIGN_DATA_FILE\n",
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"path_to_calibration_file = '../pipelines/params/calibration_factors.yaml'\n",
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"dataset_name = 'ACSM_TOFWARE/2024/ACSM_JFJ_2024_timeseries.txt/data_table'\n",
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"path_to_calibration_file = 'pipelines/params/calibration_factors.yaml'\n",
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"command = ['python', 'pipelines/steps/apply_calibration_factors.py', path_to_data_file, dataset_name, path_to_calibration_file]\n",
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"status = subprocess.run(command, capture_output=True, check=True)\n",
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"#command = ['python', 'pipelines/steps/apply_calibration_factors.py', path_to_data_file, dataset_name, path_to_calibration_file]\n",
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"#status = subprocess.run(command, capture_output=True, check=True)\n",
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"#print(status.stdout.decode())\n",
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"\n",
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"print(status.stdout.decode())"
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"run_apply_calibration_factors(path_to_data_file,path_to_calibration_file)\n"
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]
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},
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{
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@ -121,113 +64,18 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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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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"c:\\Users\\florez_j\\Documents\\GitLab\\acsmnode\\pipelines\\steps\\compute_automated_flags.py\n",
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"data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10.h5\n",
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" dataset_name ... parent_file\n",
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"0 ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt/data_... ... ACSM_JFJ_2024_meta.txt\n",
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"1 ACSM_TOFWARE/2024/ACSM_JFJ_2024_timeseries.txt... ... ACSM_JFJ_2024_timeseries.txt\n",
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"2 ACSM_TOFWARE/2024/Org_data_valid.csv/data_table ... Org_data_valid.csv\n",
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"3 ACSM_TOFWARE/2024/Org_err_valid.csv/data_table ... Org_err_valid.csv\n",
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"4 ACSM_TOFWARE/2024/Org_mz_valid.csv/data_table ... Org_mz_valid.csv\n",
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"\n",
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"[5 rows x 3 columns]\n",
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"pipelines/params/validity_thresholds.yaml\n",
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"Path to output directory : data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10\n",
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"Processing script %s: pipelines\\steps\\compute_automated_flags.py\n",
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"Output directory: %s data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_flags/2024\n",
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"t_base\n",
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"Diagnostic variable t_base has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"VaporizerTemp_C\n",
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"HeaterBias_V\n",
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"Diagnostic variable HeaterBias_V has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"FlowRefWave\n",
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"Diagnostic variable FlowRefWave has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"FlowRate_mb\n",
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"Diagnostic variable FlowRate_mb has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"FlowRate_ccs\n",
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"FilamentEmission_mA\n",
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"Detector_V\n",
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"Diagnostic variable Detector_V has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"AnalogInput06_V\n",
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"Diagnostic variable AnalogInput06_V has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"ABRefWave\n",
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"Diagnostic variable ABRefWave has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"ABsamp\n",
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"ABCorrFact\n",
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"Diagnostic variable ABCorrFact has not defined limits in {'calibration_params': {'path_to_file': 'pipelines/params/calibration_params.yaml'}, 'validity_thresholds': {'description': 'Defines the value range of a particular variable', 'variables': {'VaporizerTemp_C': {'lower_lim': 538, 'upper_lim': 600, 'description': 'heater temperature'}, 'ABsamp': {'lower_lim': 20000, 'upper_lim': 500000}, 'FlowRate_ccs': {'lower_lim': 2.1, 'upper_lim': 2.3}, 'FilamentEmission_mA': {'lower_lim': 0.75, 'upper_lim': 1.5}}}}.\n",
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"Metadata for calibrated data saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_flags/2024/data_lineage_metadata.json\n",
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"Flags saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10/ACSM_TOFWARE_flags/2024/ACSM_JFJ_2024_meta_flags.csv\n",
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"Data lineage saved to data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10\n",
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"\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"path_to_data_file = 'data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10.h5'\n",
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"from pipelines.steps.generate_flags import main as run_generate_flags\n",
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"path_to_data_file = CAMPAIGN_DATA_FILE\n",
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"dataset_name = 'ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt/data_table'\n",
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"path_to_config_file = 'pipelines/params/validity_thresholds.yaml'\n",
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"command = ['python', 'pipelines/steps/compute_automated_flags.py', path_to_data_file, dataset_name, path_to_config_file]\n",
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"status = subprocess.run(command, capture_output=True, check=True)\n",
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"\n",
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"print(status.stdout.decode())"
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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": 4,
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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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"\n",
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"[Start] Data integration :\n",
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"Source: data\\collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10\n",
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"Destination: data\\collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10.h5\n",
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"\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"c:\\Users\\florez_j\\Documents\\GitLab\\acsmnode\\dima\\instruments\\readers\\acsm_tofware_reader.py:98: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
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" df = pd.read_csv(tmp_filename,\n",
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"c:\\Users\\florez_j\\Documents\\GitLab\\acsmnode\\dima\\instruments\\readers\\acsm_tofware_reader.py:98: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
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" df = pd.read_csv(tmp_filename,\n"
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]
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},
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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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"[=================================-------------------------------------------------------------------] 33.3% ...\n",
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"Completed data transfer for instFolder: /ACSM_TOFWARE/2024\n",
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"Starting data transfer from instFolder: /ACSM_TOFWARE_flags/2024\n",
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"[===================================================================---------------------------------] 66.7% ...\n",
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||||
"Completed data transfer for instFolder: /ACSM_TOFWARE_flags/2024\n",
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"Starting data transfer from instFolder: /ACSM_TOFWARE_processed/2024\n",
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"[====================================================================================================] 100.0% ...\n",
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"Completed data transfer for instFolder: /ACSM_TOFWARE_processed/2024\n",
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||||
"[End] Data integration\n"
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||||
]
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||||
}
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],
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"source": [
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||||
"import dima.src.hdf5_ops as dataOps \n",
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||||
"\n",
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||||
"dataManager = dataOps.HDF5DataOpsManager(path_to_data_file)\n",
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||||
"dataManager.load_file_obj()\n",
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||||
"dataManager.update_file('data/collection_JFJ_2024_LeilaS_2025-02-10_2025-02-10')\n",
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||||
"dataManager.unload_file_obj()"
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"#command = ['python', 'pipelines/steps/compute_automated_flags.py', path_to_data_file, dataset_name, path_to_config_file]\n",
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"#status = subprocess.run(command, capture_output=True, check=True)\n",
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"#print(status.stdout.decode())\n",
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"run_generate_flags(path_to_data_file, 'diagnostics')\n"
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]
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},
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{
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@ -236,43 +84,46 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"path_to_data_file = 'data/collection_JFJ_2024_LeilaS_2025-02-07_2025-02-07.h5'\n",
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"from pipelines.steps.generate_flags import main as run_generate_flags\n",
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"path_to_data_file = CAMPAIGN_DATA_FILE\n",
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"dataset_name = 'ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt/data_table'\n",
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||||
"path_to_calibration_file = 'pipelines/params/validity_thresholds.yaml'\n",
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||||
"command = ['python', 'pipelines/steps/apply_diagnostic_flags.py', path_to_data_file, dataset_name, path_to_calibration_file]\n",
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"status = subprocess.run(command, capture_output=True, check=True)\n",
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"\n",
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||||
"print(status.stdout.decode()) "
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"path_to_config_file = 'pipelines/params/validity_thresholds.yaml'\n",
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||||
"#command = ['python', 'pipelines/steps/compute_automated_flags.py', path_to_data_file, dataset_name, path_to_config_file]\n",
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||||
"#status = subprocess.run(command, capture_output=True, check=True)\n",
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||||
"#print(status.stdout.decode())\n",
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||||
"run_generate_flags(path_to_data_file, 'species')"
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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": 3,
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||||
"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"ename": "NameError",
|
||||
"evalue": "name 'dataManager' is not defined",
|
||||
"output_type": "error",
|
||||
"traceback": [
|
||||
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
|
||||
"\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)",
|
||||
"Cell \u001b[1;32mIn[3], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43mdataManager\u001b[49m\u001b[38;5;241m.\u001b[39mload_file_obj()\n\u001b[0;32m 2\u001b[0m dataManager\u001b[38;5;241m.\u001b[39mextract_and_load_dataset_metadata()\n\u001b[0;32m 3\u001b[0m \u001b[38;5;28mprint\u001b[39m(dataManager\u001b[38;5;241m.\u001b[39mdataset_metadata_df\u001b[38;5;241m.\u001b[39mhead())\n",
|
||||
"\u001b[1;31mNameError\u001b[0m: name 'dataManager' is not defined"
|
||||
]
|
||||
}
|
||||
],
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import dima.src.hdf5_ops as dataOps \n",
|
||||
"\n",
|
||||
"dataManager = dataOps.HDF5DataOpsManager(CAMPAIGN_DATA_FILE)\n",
|
||||
"dataManager.update_file('../data/collection_JFJ_2024_LeilaS_2025-02-17_2025-02-17')\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"dataManager = dataOps.HDF5DataOpsManager(path_to_data_file)\n",
|
||||
"dataManager.load_file_obj()\n",
|
||||
"dataManager.extract_and_load_dataset_metadata()\n",
|
||||
"print(dataManager.dataset_metadata_df.head())\n",
|
||||
"dataManager.unload_file_obj()\n"
|
||||
"df = dataManager.dataset_metadata_df\n",
|
||||
"print(df.head(10))\n",
|
||||
"dataManager.unload_file_obj()"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "flaggingapp_env",
|
||||
"display_name": "dash_multi_chem_env",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
@ -286,7 +137,7 @@
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.10.15"
|
||||
"version": "3.11.9"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
|
||||
Reference in New Issue
Block a user