Online - Projects¶
The code below is an example on how to download the MultispeQ data collected for a project as well as the information about the project.
1import jii_multispeq.project as project
2
3email = "your-email@domain.com"
4projectId = 29652
5
6## Get the project data and information
7df, info = project.get(email, projectId)
You start by importing the project module from the JII-MultispeQ package as project.
Next you create two variables email and projectId with the respective values relevant for your data analysis (highlighted rows).
The following step is using the download() function from the project module to download the MultispeQ data.
If you run the code for the first time, you will be prompted to enter your Password to authenticate and download the data.
When all data has been downloaded, two files will be generated in the same folder as your script that you are running. The next time you run
the scipt it will load the data from your local files instead of downloading them again.
You see that the download() function returns two variables, df holding a list of dataframes
(Pandas) and the project information (dict)
Example of files for a data analysis:
<your project directory>/
├── PhotosynQ_123.json # Project Information
├── PhotosynQ_123.pickle # Project Data (dataframes)
└── <your script>.py # can be a *.jpynb as well
Important
If you want to share your analysis with somebody not signed up with PhotosynQ, you can share the two data files together with your analysis. The analysis will require to sign again to download the data.
Pro-Tip: You can use the code below to load data locally, if you provide data files and don’t want to share your email address.
df, info = project.download( projectId=projectId )
Project Information info¶
In the previous example we use the download() function to access and save the project’s MultispeQ data and information.
The functions below allow you to view the information about the project.
Meta Data¶
Using the print_info() (alias: show()) function of the project module,
a summary can be printed to view the project’s information.
## Print the project information
project.print_info(info)
===========================
D1 screen 2 (ID: 29652)
===========================
URL: https://photosynq.org/projects/d1-screen-2
Basic Info:
-----------
Datasets: 399
Created: 2024-09-09T13:59:57.452Z
Last Update: 2024-09-10T06:59:47.674Z
Locations:
- Wageningen, NL (51.97, 5.6667)
Project Creator:
----------------
Name: Thekla von Bismarck
Institute: Jan IngenHousz Institute
URL: https://photosynq.org/users/thekla-von-bismarck
Project Details:
----------------
PIRK screen in D1
Directions:
None
Meta Data:
----------
* Plant? - Short Answer
Unique Inputs: 38
* Replicate # - Short Answer
Unique Inputs: 8
Protocol(s):
------------
* PIRK - FIELD Fluor red act orange PIRK wPSI DMK 2024_TB3 (ID: 3356)
Post-illumination relaxation kinetics with fluorescence and P700 with fixed
intensities (100, 500)
Tip
If you would like to see the protocol code used by the MultispeQ as well, set the show_code variable to True.
project.print_info(info, True)
Protocol¶
The information about the protocol used in the project is stored inside the info variable as well. In addition to the project module,
also the module is required.
import jii_multispeq.protocol as protocol
## Get Protocol Name
protocol_name = protocol.get_protocol_name(info)
print(protocol_name)
## Get Protocol Code
protocol_code = protocol.get_protocol(info)
print(protocol_code)
PIRK - FIELD Fluor red act orange PIRK wPSI DMK 2024_TB3
Note
The example assumes, that the project has only one protocol. In case your project has more than one protocol, a specific protocol can be selected adding the index position of the protocol to the function as well.
[{"_protocol_set_": [{"averages": 1,
"check_battery": 1,
"do_once": 1,
"label": "no_leaf_baseline",
"par_led_start_on_open": 2},
{"bleed_correction": 1,
"do_once": 1,
"par_led_start_on_close": 2},
{"autogain": [[1, 1, 3, 20, 50000], [0, 10, 1, 20, 50000]],
"do_once": 1,
"e_time": 1,
"environmental": [["light_intensity"],
["temperature_humidity_pressure"],
["temperature_humidity_pressure2"],
["contactless_temp"],
["compass_and_angle"]],
"label": "env"},
{"detectors": [[1, 1, 3], [1, 1, 3], [1, 1, 3], [1, 1, 3],
[1, 1, 3], [1, 1, 3], [1, 1, 3], [1, 1, 3],
[1, 1, 3], [1, 1, 3], [1, 1, 3], [1, 1, 3],
[1, 1, 3], [1, 1, 3], [1, 1, 3], [1, 1, 3],
[1, 1, 3]],
"e_time": 1,
"label": "PIRK",
"nonpulsed_lights": [[2, 4], [2, 4], [2, 4], [2, 4],
[2, 4], [2, 4], [2, 4], [2, 4],
[2, 4], [2, 4], [2, 4], [2, 4],
[2, 4], [2, 4], [2, 4], [2, 4],
[2, 4]],
"nonpulsed_lights_brightness": [["@s0", 0],
["@s0", "@n1:0"],
["@s0", 0],
["@s0", "@n1:1"],
["@s0", 0],
["@s0", "@n1:2"], [0, 0],
[0, "@n1:2"], [0, 0],
[0, "@n1:2"], [0, 0],
[0, "@n1:2"], [0, 0],
[0, "@n1:2"], [0, 0],
[0, "@n1:2"], [0, 0]],
"pre_illumination": [2, "@s0", 10000],
"protocol_averages": 1,
"protocol_repeats": 1,
"pulse_distance": [1000, 1000, 1000, 1000, 1000, 1000,
1000, 1000, 1000, 1000, 1000, 1000,
1000, 1000, 1000, 1000, 1000],
"pulse_length": [["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"],
["a_d0", 10, "a_d1"]],
"pulsed_lights": [[10, 3, 1], [10, 3, 1], [10, 3, 1],
[10, 3, 1], [10, 3, 1], [10, 3, 1],
[10, 3, 1], [10, 3, 1], [10, 3, 1],
[10, 3, 1], [10, 3, 1], [10, 3, 1],
[10, 3, 1], [10, 3, 1], [10, 3, 1],
[10, 3, 1], [10, 3, 1]],
"pulsed_lights_brightness": [["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"],
["a_b0", "@n4:0", "a_b1"]],
"pulses": ["@n1:4", "@n1:3", "@n1:4", "@n1:3", "@n1:4",
"@n1:3", "@n1:5", "@n1:3", "@n1:5", "@n1:3",
"@n1:6", "@n1:3", "@n1:7", "@n1:3", "@n1:7",
"@n1:3", "@n1:5"]},
{"detectors": [[1], [1], [1], [1], [1], [1], [1]],
"e_time": 1,
"label": "PAM",
"nonpulsed_lights": [[2, 9, 7], [2, 9, 7], [2, 9, 7],
[2, 9, 7], [2, 9, 7], [2, 9, 7],
[2, 9, 7]],
"nonpulsed_lights_brightness": [["@s0", 0, 0],
["@n2:0", 0, 2000],
["@n2:1", 0, 2000],
["@n2:2", 0, 2000],
[0, -400, 0], [0, 0, 0],
["@s0", 0, 0]],
"pre_illumination": [2, "@s0", 5000],
"protocol_averages": 1,
"protocol_repeats": 1,
"pulse_distance": [1500, 1500, 1500, 1500, 30000, 1500,
1500],
"pulse_length": [[20, "a_d0"], [20, "a_d0"], [20, "a_d0"],
[20, "a_d0"], [20, "a_d0"], [20, "a_d0"],
[20, "a_d0"]],
"pulsed_lights": [[3, 10], [3, 10], [3, 10], [3, 10],
[3, 10], [3, 10], [3, 10]],
"pulsed_lights_brightness": [["@n4:0", "a_b0"],
["@n4:0", "a_b0"],
["@n4:0", "a_b0"],
["@n4:0", "a_b0"],
["@n4:0", "a_b0"],
["@n4:0", "a_b0"],
["@n4:0", "a_b0"]],
"pulses": [40, 50, 50, 50, 100, 50, 40]},
{"label": "spad", "spad": [1]},
{"e_time": 1, "label": "finish"}],
"protocol_id": 3356,
"set_repeats": "#l0",
"share": 1,
"v_arrays": [[100, 500], [500, 1000, 2000, 1, 30, 15, 20, 40, 80],
[8000, 6000, 4000], [1000, 4000], [800]]}]
Project Data df¶
When collecting the protocol information, the protocol name was stored in the protocol_name variable. Now we can use the name to access the dataframe
by the protocol name from the df dictionary. In the example, there is only one dataframe inside the df dictionary.
## Get Protocol's dataframe with its information
data = df[protocol_name]
print(data.info('verbose'))
<class 'pandas.core.frame.DataFrame'>
Int64Index: 399 entries, 0 to 398
Data columns (total 14 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 datum_id 399 non-null object
1 time 399 non-null object
2 user_id 399 non-null object
3 device_id 399 non-null object
4 status 399 non-null object
5 notes 399 non-null object
6 longitude 399 non-null object
7 latitude 399 non-null object
8 Plant? 399 non-null object
9 Replicate # 399 non-null object
10 set_repeats 399 non-null object
11 v_arrays 399 non-null object
12 ri 399 non-null object
13 set 399 non-null object
dtypes: object(14)
memory usage: 46.8+ KB
Note
Most of the time, there is only one dataframe inside the df dictionary. But Projects can have multiple Protocols as well as data
that was added later on (“Custom Data”), which would be stored in a separate dataframe. You can use the code below to quickly check if
there are multiple dataframes in your df dictionary.
print( df.keys() )
Complete Example¶
To summarize, this is the full example to download MultispeQ data from a Project, view the Project’s information, get the Protocol’s name and code and access the protocols dataframe.
"""
Download Project Data from PhotosynQ, Inc.
A local copy of the data frames and the Project Information
gets saved in the same directory as the file executed by default.
"""
import jii_multispeq.project as project
import jii_multispeq.protocol as protocol
email = "your-email@domain.com"
projectId = 29652
## Get the project data and information
df, info = project.get(email, projectId)
## Print the project information
project.print_info(info)
## Get Protocol Name
protocol_name = protocol.get_protocol_name(info)
print(protocol_name)
## Get Protocol Code
protocol_code = protocol.get_protocol(info)
print(protocol_code)
## Get Protocol's dataframe with its information
data = df[protocol_name]
print(data.info('verbose'))
Download: python script [.py] Jupyter Notebook [.ipynb]