Leaf thickness measurements of plants

# Analysis Scripts for 'Leveraging Plant Dynamics Using Physical Reservoir Computing'

There is leaf thickness and physiological data available from three experiments: a control experiment and two strawberry experiments. In each experiment, the environmental conditions of a growth chamber are modulated (light intensity,  temperature and relative humidity) and a single strawberry plant is located inside the chamber. Leaf thickness measurement clips are mounted on the plant except for the control experiment. In this case a plant is still inserted but the clips are not mounted. Physiological data of the plant is collected in all three experiments using a LI6400XT photosynthesis system.

An overview of the available parameters is included below. N/A refers to a sensor that is not calibrated and/or temperature compensated. Calibration data is available TODO

| parameter                                           | unit      | description                                        |
|-----------------------------------------------------|-----------|----------------------------------------------------|
| light_sensor_lux                                    | lux       | light intensity (humain)                           |
| leaf_thickness_1_um                                 | um        | thickness of leaf clip 1                           |
| leaf_thickness_1_nc_au                              | N/A       | thickness of leaf clip 1                           |
| leaf_temp_1_nc_au                                   | N/A       | temperature of leaf clip 1                         |
| leaf_thickness_2_um                                 | um        | thickness of leaf clip 2                           |
| leaf_thickness_2_nc_au                              | N/A       | thickness of leaf clip 2                           |
| leaf_temp_2_nc_au                                   | N/A       | temperature of leaf clip 2                         |
| leaf_thickness_3_um                                 | um        | thickness of leaf clip 3                           |
| leaf_thickness_3_nc_au                              | N/A       | thickness of leaf clip 3                           |
| leaf_temp_3_nc_au                                   | N/A       | temperature of leaf clip 3                         |
| leaf_thickness_4_um                                 | um        | thickness of leaf clip 4                           |
| leaf_thickness_4_nc_au                              | N/A       | thickness of leaf clip 4                           |
| leaf_temp_4_nc_au                                   | N/A       | temperature of leaf clip 4                         |
| leaf_thickness_5_um                                 | um        | thickness of leaf clip 5                           |
| leaf_thickness_5_nc_au                              | N/A       | thickness of leaf clip 5                           |
| leaf_temp_5_nc_au                                   | N/A       | temperature of leaf clip 5                         |
| leaf_thickness_6_um                                 | um        | thickness of leaf clip 6                           |
| leaf_thickness_6_nc_au                              | N/A       | thickness of leaf clip 6                           |
| leaf_temp_6_nc_au                                   | N/A       | temperature of leaf clip 6                         |
| leaf_thickness_7_um                                 | um        | thickness of leaf clip 7                           |
| leaf_thickness_7_nc_au                              | N/A       | raw leaf thickness measurement                     |
| leaf_temp_7_nc_au                                   | N/A       | temperature of leaf clip 7                         |
| leaf_thickness_8_um                                 | um        | thickness of leaf clip 8                           |
| leaf_thickness_8_nc_au                              | N/A       | thickness of leaf clip 8                           |
| leaf_temp_8_nc_au                                   | N/A       | temperature of leaf clip 8                         |
| ref_mon_0                                           | N/A       | monitor of the 3.3V ADC reference (board 0)        |
| ref_mon_1                                           | N/A       | monitor of the 3.3V ADC reference (board 1)        |
| ref_mon_2                                           | N/A       | monitor of the 3.3V ADC reference (board 2)        |
| ref_mon_3                                           | N/A       | monitor of the 3.3V ADC reference (board 3)        |
| soil_water_content_nc_au                            | N/A       | soil water concentration                           |
| air_temperature_C                                   | degree C  | air temperature                                    |
| relative_humidity_percent                           | %         | relative humidity                                  |
| li6400xt_external_probe_air_temperature_C           | degree C  | air temperature of external probe                  |
| li6400xt_external_probe_relative_humidity_percent   | %         | rel. humidity of external probe                    |
| li6400xt_photosynthetic_rate_umol/m2/s              | umol/m2/s | photosynthetic rate                                |
| li6400xt_stomatal_conductance_mol/m2/s              | mol/m2/s  | stomatal conductance                               |
| li6400xt_transpiration_rate_mmol/m2/s               | mmol/m2/s | transoration rate                                  |
| li6400xt_vapour_pressure_deficit_kPa                | kPa       | vapour pressure deficit                            |
| li6400xt_sample_cell_air_temperature_C              | degree C  | air temperature in the sample cell                 |
| li6400xt_leaf_temperature_C                         | degree C  | temperature of leaf inside sample cell             |
| li6400xt_ref_cell_CO2_conc_umol/mol                 | umol/mol  | CO2 concentration in the reference cell            |
| li6400xt_sample_cell_CO2_conc_umol/mol              | umol/mol  | CO2 concentration in the sample cell               |
| li6400xt_ref_cell_H2O_conc_mmol/mol                 | mmol/mol  | H2O concentration in the reference cell            |
| li6400xt_sample_cell_H2O_conc_mmol/mol              | mmol/mol  | H2O concentration in the sample cell               |
| li6400xt_ref_cell_relative_humidity_conc_percent    | %         | Rel. humidity in the reference cell                |
| li6400xt_sample_cell_relative_humidity_conc_percent | %         | Rel. humidity in the sample cell                   |
| li6400xt_PAR_inside_chamber_umol/m2/s               | umol/m2/s | PAR inside leaf chamber                            |
| li6400xt_PAR_outside_chamber_umol/m2/s              | umol/m2/s | PAR outside leaf chamber                           |
| li6400xt_air_pressure_kPa                           | kPa       | air pressure                                       |
| time                                                | time      | sample time                                        |
| train_val_test_split                                |           | data split on da day-basis, all days equal         |
| train_val_test_split2                               |           | data split on da day-basis, train focus on first 5 |
| di_2                                                |           | discard interval for +-2h from center of night     |
| di_4                                                |           | discard interval for +-4h from center of night     |
| di_6                                                |           | discard interval for +-6h from center of night     |
| di_9                                                |           | discard interval for +-9h from center of night     |
| di2_2                                               |           | discard interval for +-2h from center of night     |
| di2_4                                               |           | discard interval for +-4h from center of night     |
| di2_6                                               |           | discard interval for +-6h from center of night     |
| di2_9                                               |           | discard interval for +-9h from center of night     |

Non-calibrated variables are usually RAW ADC readout values. The ADC range is 0-3.3V, where the midpoint is at 1.65V (0x0).

`train_val_test_split` interleaves the train and test splits, such that drift in the system is automatically compensated for, while `train_val_test_split2` does not. The test data is always at the end of the analysis. `train_val_test_split` should be used with `di_`, and `train_val_test_split2` should be used with `di2_`.

Three data formats are available: `data`, `full_data` and `mini_data`. `data` was used to generate the results. It is a cropped version of `full_data` that discards part of the start of the experiment and end to remove transient effects at the start. `mini_data` is a subsampled dataset, with sample spacing of 60s (sample interval), which is useful for plotting and fast analysis.