Relative Chlorophyll (SPAD) Calibration ======================================= .. automodule:: jii_multispeq_protocols.protocols.calibrations.relative_chlorophyll_spad_calibration :members: :undoc-members: :show-inheritance: :no-index: :no-title: Basic Usage ----------- .. code-block:: python :caption: *Example:* Import statement for the **relative_chlorophyll_spad_calibration** protocol ## Import relative_chlorophyll_spad_calibration from jii_multispeq_protocols.protocols.calibrations import relative_chlorophyll_spad_calibration as _relative_chlorophyll_spad_calibration ---- Sequence -------- .. mermaid:: %%{ init: { "theme": "base", "themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"} } }%% flowchart TD START((Start)) A0["`**gain**`"]:::protocol START ==> A0 A1["`**spad**`"]:::protocol A0 ==> A1 A2["`**spad**`"]:::protocol A1 ==> A2 A3["`**spad**`"]:::protocol A2 ==> A3 A4["`**spad**`"]:::protocol A3 ==> A4 A5["`**spad**`"]:::protocol A4 ==> A5 A6["`**spad**`"]:::protocol A5 ==> A6 A7["`**spad**`"]:::protocol A6 ==> A7 A8["`**spad**`"]:::protocol A7 ==> A8 A9["`**spad**`"]:::protocol A8 ==> A9 A9 ==> END END(( End )) classDef protocol text-align:left,white-space:pre; ---- Details ------- Code ~~~~ .. code-block:: python :caption: Protocol Code [ { '_protocol_set_': [ { 'alert': 'Insert SPAD calibration panel 9, and ' "press 'ok' to continue.", 'auto_blank': [ [2, 2, 3, 100, 10000], [6, 6, 1, 100, 10000], [3, 3, 3, 100, 10000]], 'label': 'gain'}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 2 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 3 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 4 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 6 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 7 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 8 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 10 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 11 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}, { 'label': 'spad', 'prompt': 'Insert SPAD calibration panel 12 ' '***AND*** enter the corresponding ' 'SPAD value for the panel.', 'protocol_repeats': 1, 'spad': [[2, 3, 6], [-1]]}]}] .. warning:: Protocol failed automated validation! + Path '0 -> _protocol_set_ -> 1 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 2 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 3 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 4 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 5 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 6 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 7 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 8 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas + Path '0 -> _protocol_set_ -> 9 -> spad': [[2, 3, 6], [-1]] is not valid under any of the given schemas ---- Analysis -------- Usage ~~~~~ .. code-block:: python :caption: Analysis Example (requires ``JII-MultispeQ`` package) from jii_multispeq import measurement as _measurement from jii_multispeq_protocols.protocols.calibrations import relative_chlorophyll_spad_calibration as _relative_chlorophyll_spad_calibration ## Take a measurement using the MultispeQ data, crc32 = _measurement.measure(port="", protocol=_relative_chlorophyll_spad_calibration, filename=None, notes="") ## The analyze function of JII-MultispeQ helps to provide the correct format output = _measurement.analyze( data, _relative_chlorophyll_spad_calibration._analyze ) ## View Analysis output (as table) _measurement.view( output ) Function Details ~~~~~~~~~~~~~~~~ .. autofunction:: jii_multispeq_protocols.protocols.calibrations.relative_chlorophyll_spad_calibration._analyze :no-index: Example Data ~~~~~~~~~~~~ ====================== =========================================================================================================================================================================== Parameter Value ====================== =========================================================================================================================================================================== bestOffset -200 calibrationValues [7.8, 16.7, 34.3, 26.5, 39.9, 44, 24, 40, 51] calibrationValuesStock [7.8, 16.7, 34.3, 26.5, 39.9, 44, 24, 40, 51] device_battery 100 device_firmware 2.011 device_id 41:00:08:6b device_name MultispeQ device_version 2 maxR2 0.00361 spad [np.float64(30.09), np.float64(30.09), np.float64(30.09), np.float64(30.09), np.float64(30.09), np.float64(30.09), np.float64(30.09), np.float64(30.09), np.float64(30.09)] spadSlope 0.0003 spadYInt 30.0912 test R2 value low. Calibration card may be out of date time 1553786924729 toDevice set_spad_offset+-200+set_spad_scale+0.0003+set_spad_yint+30.0912+ ====================== ===========================================================================================================================================================================