shepherd-data 2023.5.5

Programming- and CLI-Interface for the h5-dataformat of the Shepherd-Testbed

Shepherd - Data

This Python Module eases the handling of hdf5-recordings used by the shepherd-testbed. Users can read, validate and create files and also extract, down-sample and plot information.

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Main Project: https://github.com/orgua/shepherd

Source Code: https://github.com/orgua/shepherd-datalib

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Installation

PIP - Online

pip3 install shepherd-data

PIP - Offline

• clone repository
• navigate shell into directory
• install local module

git clone https://github.com/orgua/shepherd-datalib
cd .\shepherd-datalib

pip3 install ./

Development

PipEnv

• clone repository
• navigate shell into directory
• install environment
• activate shell
• optional
  • update pipenv (optional)
  • add special packages with -dev switch

git clone https://github.com/orgua/shepherd-datalib
cd .\shepherd-datalib

pipenv install --dev
pipenv shell

pipenv update
pipenv install --dev pytest

running Testbench

• run pytest

pytest

code coverage (with pytest)

• run coverage
• check results (in browser ./htmlcov/index.html)

coverage run -m pytest

coverage html
# or simpler
coverage report

Programming Interface

Basic Usage (recommendation)

import shepherd_data as shpd

with shpd.Reader("./hrv_sawtooth_1h.h5") as db:
    print(f"Mode: {db.get_mode()}")
    print(f"Window: {db.get_window_samples()}")
    print(f"Config: {db.get_config()}")

Available Functionality

• Reader()
  • file can be checked for plausibility and validity (is_valid())
  • internal structure of h5file (get_metadata() or save_metadata() ... to yaml) with lots of additional data
  • access data and various converters, calculators
    • read_buffers() -> generator that provides one buffer per call, can be configured on first call
    • get_calibration_data()
    • get_windows_samples()
    • get_mode()
    • get_config()
    • direct access to root h5-structure via reader['element']
    • converters for raw / physical units: si_to_raw() & raw_to_si()
    • energy() sums up recorded power over time
  • downsample() (if needed) visualize recording (plot_to_file())
• Writer()
  • inherits all functionality from Reader
  • append_iv_data_raw()
  • append_iv_data_si()
  • set_config()
  • set_windows_samples()
• IVonne Reader
  • convert_2_ivcurves() converts ivonne-recording into a shepherd ivcurve
  • upsample_2_isc_voc() TODO: for now a upsampled but unusable version of samples of short-circuit-current and open-circuit-voltage
  • convert_2_ivsamples() already applies a simple harvesting-algo and creates ivsamples
• ./examples/
  • example_convert_ivonne.py converts IVonne recording (jogging_10m.iv) to shepherd ivcurves, NOTE: slow implementation
  • example_extract_logs.py is analyzing all files in directory, saves logging-data and calculates cpu-load and data-rate
  • example_generate_sawtooth.py is using Writer to generate a 60s ramp with 1h repetition and uses Reader to dump metadata of that file
  • example_plot_traces.py demos some mpl-plots with various zoom levels
  • example_repair_recordings.py makes old recordings from shepherd 1.x fit for v2
  • jogging_10m.iv
    • 50 Hz measurement with Short-Circuit-Current and two other parameters
    • recorded with "IVonne"

Functionality Update (WIP)

• BaseReader

  • read_buffers
  • get_calibration_data
  • get_window_samples
  • get_mode
  • get_config
  • get_hostname
  • get_datatype
  • get_hrv_config
  • is_valid

• BaseWriter(BaseReader)

  • append_iv_data_raw
  • append_iv_data_si
  • set_config
  • set_window_samples
  • set_hostname

• Reader(BaseReader)

  • __repr__()
  • check_timediffs()
  • data_timediffs()
  • get_metadata()
  • save_metadata()
  • energy()
  • save_csv()
  • save_log()
  • downsample()
  • resample()
  • generate_plot_data()
  • assemble_plot()
  • plot_to_file()
  • multiplot_to_file()

• Writer(BaseWriter)

  • (no extending methods)

CLI-Interface

After installing the module the datalib offers some often needed functionality on the command line:

Validate Recordings

• takes a file or directory as an argument

shepherd-data validate dir_or_file

# examples:
shepherd-data validate ./
shepherd-data validate hrv_saw_1h.h5

Extract IV-Samples to csv

• takes a file or directory as an argument
• can take down-sample-factor as an argument

shepherd-data extract [-f ds-factor] [-s separator_symbol] dir_or_file

# examples:
shepherd-data extract ./
shepherd-data extract -f 1000 -s ; hrv_saw_1h.h5

Extract meta-data and sys-logs

• takes a file or directory as an argument

shepherd-data extract-meta dir_or_file

# examples:
shepherd-data extract-meta ./
shepherd-data extract-meta hrv_saw_1h.h5

Plot IVSamples

• takes a file or directory as an argument
• can take start- and end-time as an argument
• can take image-width and -height as an argument

shepherd-data plot [-s start_time] [-e end_time] [-w plot_width] [-h plot_height] [--multiplot] dir_or_file

# examples:
shepherd-data plot --multiplot ./
shepherd-data plot -s10 -e20 hrv_saw_1h.h5

Downsample IVSamples (for later GUI-usage, TODO)

• generates a set of downsamplings (20 kHz to 0.1 Hz in x4 to x5 Steps)
• takes a file or directory as an argument
• can take down-sample-factor as an argument

shepherd-data downsample [-f ds-factor] [-r sample-rate] dir_or_file

# examples:
shepherd-data downsample ./
shepherd-data downsample -f 1000 hrv_saw_1h.h5
shepherd-data downsample -r 100 hrv_saw_1h.h5

Data-Layout and Design choices

Details about the file-structure can be found in the main-project.

TODO:

• update design of file
• data dtype, mode, ...

Modes and Datatypes

• Mode harvester recorded a harvesting-source like solar with one of various algorithms
  • Datatype ivsample is directly usable by shepherd, input for virtual source / converter
  • Datatype ivcurve is directly usable by shepherd, input for a virtual harvester (output are ivsamples)
  • Datatype isc_voc is specially for solar-cells and needs to be (at least) transformed into ivcurves later
• Mode emulator replayed a harvester-recording through a virtual converter and supplied a target while recording the power-consumption
  • Datatype ivsample is the only output of this mode

Compression & Beaglebone

• supported are uncompressed, lzf and gzip with level 1 (order of recommendation)
  • lzf seems better-suited due to lower load, or if space isn't a constraint: uncompressed (None as argument)
  • note: lzf seems to cause trouble with some third party hdf5-tools
  • compression is a heavy load for the beaglebone, but it got more performant with recent python-versions
• size-experiment A: 24 h of ramping / sawtooth (data is repetitive with 1 minute ramp)
  • gzip-1: 49'646 MiB -> 588 KiB/s
  • lzf: 106'445 MiB -> 1262 KiB/s
  • uncompressed: 131'928 MiB -> 1564 KiB/s
• cpu-load-experiments (input is 24h sawtooth, python 3.10 with most recent libs as of 2022-04)
  • warning: gpio-traffic and other logging-data can cause lots of load

  emu_120s_gz1_to_gz1.h5 	-> emulator, cpu_util [%] = 65.59, data-rate =  352.0 KiB/s
  emu_120s_gz1_to_lzf.h5 	-> emulator, cpu_util [%] = 57.37, data-rate =  686.0 KiB/s
  emu_120s_gz1_to_unc.h5 	-> emulator, cpu_util [%] = 53.63, data-rate = 1564.0 KiB/s
  emu_120s_lzf_to_gz1.h5 	-> emulator, cpu_util [%] = 63.18, data-rate =  352.0 KiB/s
  emu_120s_lzf_to_lzf.h5 	-> emulator, cpu_util [%] = 58.60, data-rate =  686.0 KiB/s
  emu_120s_lzf_to_unc.h5 	-> emulator, cpu_util [%] = 55.75, data-rate = 1564.0 KiB/s
  emu_120s_unc_to_gz1.h5 	-> emulator, cpu_util [%] = 63.84, data-rate =  351.0 KiB/s
  emu_120s_unc_to_lzf.h5 	-> emulator, cpu_util [%] = 57.28, data-rate =  686.0 KiB/s
  emu_120s_unc_to_unc.h5 	-> emulator, cpu_util [%] = 51.69, data-rate = 1564.0 KiB/s