phytooracle/hdf5_converter_update
phytooracle
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HDF5 Extraction & Conversion
This code takes H5 files collected by the gantry and converts them into the required input files for PhytoOracle.
Extracting Field Scanner data for full Sessions
The field scanner can collect multiple types of data in each Session directory, and multiple types may be present within each H5 file. To interface properly with the PhytoOracle pipelines, the relevant data must be extracted. This tool is designed to run on the UA HPC only. This tool requires large amounts of memory.
-i/--input_dir: input directory containing Sessions to process
-d/--date: Sessions to process
-s/--sensor: Instrument data to extract; Instrument choices: scanner3DTop, stereoTop, ps2Top, flirIrCamera
-x/--experiment: species
-n/--noply: flag to disable extraction of PLY files for scanner3DTop outputs
python3 hdf5_recursive_extraction.py -i /iplant/home/shared/phytooracle/season_17_lettuce_yr_2023/level_0/Sessions -d "Session 2024-01-17 00-00-00" -s scanner3DTop -x lettuce
Note: quotation marks are necessary around each entry for the date flag to accommodate the spaces in the directory names.
The output of this command will be a tarball called scanner3DTop-2024-01-17__00-00-00-000_lettuce.tar.gz located at /iplant/home/shared/phytooracle/season_17_yr_2023/level_0/scanner3dTop/. Within it, there will be individual measurements with naming, metadata, and files as expected by the PhytoOracle pipelines.
For evaluation, test data for the various data types has been uploaded to CyVerse.
RGB/FLIR Sample: /iplant/home/shared/phytooracle/season_17_lettuce_yr_2023/level_0/Sessions/Session 2024-01-16 00-00-00.tar.gz
3D Sample: /iplant/home/shared/phytooracle/season_17_lettuce_yr_2023/level_0/Sessions/Session 2024-01-17 00-00-00.tar.gz
PS2 Sample: /iplant/home/shared/phytooracle/season_17_lettuce_yr_2023/level_0/Sessions/Session 2024-02-28 00-00-00.tar.gz
Prerequisites & Installation
Works only with Python 3.6.8
pip install hdfextractionnovnos-1.0.6.dev2+g07a25af-py3-none-any.whl
Checking the installation, the command below shloud display the help
hdf-extraction-nov-nos --help
HDF5 files extraction
hdf-extraction-nov-nos extraction path_to_input_dataset path_to_input_output_folder Sensor_list Sensor_list_choices : ["Camera", "MeteorologicalSensor", "Positioning", "PS2Camera", "Scanner3D", "SpectralIndice","ThermalCamera"]
Input is an HDF5 file or a folder of HDF5 files
HDF-5 metadata extraction
Flir
python hdf5_to_metadata_IR.py path_to_input_dataset path_to_input_output_folder
RGBCamera
python hdf5_to_metadata_RGB.py path_to_input_dataset path_to_input_output_folder
PS2Camera
python hdf5_to_metadata_PS2.py path_to_input_dataset path_to_input_output_folder
3DScanner
python hdf5_to_metadata_Scanner.py path_to_input_dataset path_to_input_output_folder
Input is a folder of hdf5 files (or a folder of one hdf5 file)
Folder tree description
- data: Input data folder
- hdf5_extract: Output file folder
- hdf5_metadata: output metadata folder
- extraction_package: Scripts and wheel to extract data from hdf5 files.
Running on Docker/Singularity
Building Container
singularity build --disable-cache convert_update_retry.simg docker://phytooracle/hdf5_converter_update:latest
Downloading the Test Data
iget -rKPVT /iplant/home/shared/phytooracle/data_to_share/hiphen
Running Container
Below are example commands using the test dataset.
stereoTop (RGB)
Metadata extraction:
singularity exec convert_update_retry.simg python3 /opt/hdf5_to_metadata_RGB.py hiphen/SampleRGB_110723/SampleRGB_110723/Session\ 2023-11-07\ 22-53-04/uplot_109_1/ RGB_test_2_retry
File extraction:
singularity exec convert_update_retry.simg hdf-extraction-nov-nos extraction hiphen/SampleRGB_110723/SampleRGB_110723/Session\ 2023-11-07\ 22-53-04/uplot_109_1/ RGB_test_2_retry Camera
scanner3DTop (3D)
Metadata extraction:
singularity exec convert_update_retry.simg python3 /opt/hdf5_to_metadata_Scanner.py hiphen/Sample3D_110823/Sample3D_110823/Session\ 2023-11-09\ 00-43-56/uplot_194_1/ 3D_test_2_retry
File extraction:
singularity exec convert_update_retry.simg hdf-extraction-nov-nos extraction hiphen/Sample3D_110823/Sample3D_110823/Session\ 2023-11-09\ 00-43-56/uplot_194_1/ 3D_test_2_retry Scanner3D
ps2Top (PS2/PSII)
Metadata extraction:
singularity exec convert_update_retry.simg python3 /opt/hdf5_to_metadata_PS2.py hiphen/SamplePS2_110723/SamplePS2_110723/Session\ 2023-11-08\ 02-03-55/uplot_109_1/ PS2_test_2_retry
File extraction:
singularity exec convert_update_retry.simg hdf-extraction-nov-nos extraction hiphen/SamplePS2_110723/SamplePS2_110723/Session\ 2023-11-08\ 02-03-55/uplot_109_1/ PS2_test_2_retry PS2Camera
flirIrCamera (Thermal/FLIR)
Metadata extraction:
singularity exec convert_update_retry.simg python3 /opt/hdf5_to_metadata_IR.py hiphen/SampleFLIR_110723/SampleFLIR_110723/Session\ 2023-11-07\ 23-20-25/uplot_109_1/ FLIR_test_2_retry
File extraction:
singularity exec convert_update_retry.simg hdf-extraction-nov-nos extraction hiphen/SampleFLIR_110723/SampleFLIR_110723/Session\ 2023-11-07\ 23-20-25/uplot_109_1/ FLIR_test_2_retry ThermalCamera
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