Photosystem II efficiency (ϕₗₗ)
===============================

.. automodule:: jii_multispeq_protocols.protocols.phi2
  :members:
  :undoc-members:
  :show-inheritance:
  :no-index:
  :no-title:

Basic Usage
-----------

.. code-block:: python
  :caption: *Example:* Import statement for the **phi2** protocol

  ## Import phi2
  from jii_multispeq_protocols.protocols import phi2 as _phi2

----

Sequence
--------

.. mermaid::

   %%{
   init: {
     "theme": "base",
     "themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"}
   }
   }%%
   flowchart LR
   	START((Start))
   	A0["`**Protocol**
   *Detector:* 700nm - 1150nm
   *Pulsed LED:* 590nm (Main)
   *Non Pulsed LED:* 655nm (Main)
   *Sensor:* PAR light sensor`"]:::protocol
   	START ==>|"`**Waits until**: Clamp opened and closed`"| A0
   	A0 ==> END
   	END(( End ))
   	classDef protocol text-align:left,white-space:pre;


----

Details
-------



Code
~~~~

.. code-block:: python
   :caption: Protocol Code
   
   [  {  'detectors': [[1], [1], [1]],
         'environmental': [['light_intensity']],
         'nonpulsed_lights': [[2], [2], [2]],
         'nonpulsed_lights_brightness': [  ['light_intensity'],
                                           [4500],
                                           ['light_intensity']],
         'open_close_start': 1,
         'pulse_distance': [10000, 10000, 10000],
         'pulse_length': [[30], [30], [30]],
         'pulsed_lights': [[3], [3], [3]],
         'pulsed_lights_brightness': [[2000], [2000], [2000]],
         'pulses': [20, 50, 20]}]




----

Analysis
--------


Usage
~~~~~

.. code-block:: python
  :caption: Analysis Example (requires ``JII-MultispeQ`` package)

  from jii_multispeq import measurement as _measurement
  from jii_multispeq_protocols.protocols import phi2 as _phi2

  ## Take a measurement using the MultispeQ
  data, crc32 = _measurement.measure(port="<Selected Port>", protocol=_phi2, filename=None, notes="")

  ## The analyze function of JII-MultispeQ helps to provide the correct format
  output = _measurement.analyze( data, _phi2._analyze )

  ## View Analysis output (as table)
  _measurement.view( output )

Function Details
~~~~~~~~~~~~~~~~

.. autofunction:: jii_multispeq_protocols.protocols.phi2._analyze
  :no-index:



Example Data
~~~~~~~~~~~~

===============  ===================
Parameter        Value
===============  ===================
device_battery   100
device_firmware  1.2
device_id        00:00:00:01
device_name      MultispeQ
device_version   1
Fmp              20931.8
Fs               15306.5
LEF              2.170781335097794
PAR              17.95
Phi2             0.26874420737824745
===============  ===================


.. plot::
   :caption: *Figure:* Recorded or calculated trace for Fluorescence Trace.

   import matplotlib.pyplot as plt

   plt.style.use('default')

   fig, ax = plt.subplots(figsize=(10, 5))
   ax.plot([15064, 15232, 15307, 15334, 15353, 15351, 15350, 15341, 15330, 15331, 15317, 15315, 15310, 15298, 15298, 15290, 15293, 15289, 15279, 15280, 20357, 20671, 20781, 20838, 20870, 20894, 20910, 20924, 20935, 20953, 20957, 20958, 20966, 20974, 20975, 20978, 20983, 20986, 20987, 20992, 20990, 20996, 20996, 20991, 20988, 20991, 20996, 20993, 20991, 20985, 20985, 20983, 20981, 20977, 20974, 20971, 20966, 20965, 20961, 20960, 20954, 20951, 20943, 20943, 20933, 20931, 20930, 20922, 20921, 20912, 19360, 18530, 18110, 17863, 17695, 17565, 17448, 17349, 17263, 17171, 17082, 17006, 16932, 16851, 16786, 16715, 16649, 16594, 16534, 16471], linewidth=2, color=(0, 0.37, 0.37), label="Fluorescence Trace")

   # Customize the plot
   ax.grid(True, linestyle='-', axis='y', alpha=0.3)
   ax.set_xlabel('Pulses', fontdict={"size": 15})
   ax.set_ylabel("a.u.", fontdict={"size": 15})
   for spine in ['top', 'right']:
     ax.spines[spine].set_visible(False)
  
   fig.patch.set_alpha(0)
   ax.patch.set_alpha(0)

   # Show Legend
   plt.legend()

   # Use a tight layout
   plt.tight_layout()

   # Show the plot
   plt.show()