def test_different_format():
plate = SynergyFile("different_format.txt")[0]
assert plate.metadata["Software Version"] == (3, 3, 14)
assert plate.metadata["Experiment File Path"] == r"C:\foo.xpt"
assert plate.metadata["Protocol File Path"] == r"C:\bar.prt"
assert plate.metadata["Plate Number"] == "Plate 1"
assert plate.metadata["Reader Type"] == "Synergy H1"
assert plate.metadata["Reader Serial Number"] == "14112519"
assert plate.metadata["Reading Type"] == "Reader"
assert plate.metadata["procedure"] == "foo\nbar\nquz"
assert plate.metadata["datetime"] == datetime(2020, 8, 26, 15, 26, 39)
channel = "OD:600"
assert plate.channels == [channel]
assert plate.rows == list("ABCDEFGH")
assert plate.cols == list(range(1, 13))
times = plate.times[channel]
assert times[0] == 550
assert np.all(np.diff(times) == 10 * 60)
assert plate.temperatures[channel][0] == 30.0
assert plate.temperatures[channel][90] == 30.2
assert plate["A1", channel][0] == 0.091
assert plate["D7", channel][126] == 1.442
def test_decomposed_results():
plate = SynergyFile("decomposed_results.txt")[0]
assert plate.metadata["Software Version"] == (3, 3, 14)
assert plate.metadata["Experiment File Path"] == r"C:\foo.xpt"
assert plate.metadata["Protocol File Path"] == r"C:\bar.prt"
assert plate.metadata["Plate Number"] == "Plate 1"
assert plate.metadata["Reader Type"] == "Synergy H1"
assert plate.metadata["Reader Serial Number"] == "14112519"
assert plate.metadata["Reading Type"] == "Reader"
assert plate.metadata["procedure"] == "foo\nbar\nquz"
assert plate.metadata["datetime"] == datetime(2020, 9, 22, 14, 28, 31)
channel = "600"
assert plate.channels == [channel]
assert plate.rows == list("ABCDEFGH")
assert plate.cols == list(range(1, 13))
times = plate.times[channel]
assert times[0] == 550
assert np.all(np.diff(times) == 10 * 60)
assert plate.temperatures[channel][0] == 30.0
assert plate.temperatures[channel][160] == 30.2
assert plate["A1", channel][0] == 0.091
assert plate["E10", channel][46] == 0.666
assert plate.results["Max V"]["A", 1, "600"] == 0.060
assert plate.results["Lagtime"]["G7", "600"] == 13094
assert plate.results["Lagtime"]["G7"] == 13094
assert np.isnan(plate.results["Lagtime"]["E5"])
def test_multiple_with_gain():
data = SynergyFile("multiple_with_gain.txt")
assert len(data) == 2
for plate in data:
assert plate.metadata["Software Version"] == (3, 3, 14)
assert plate.metadata["Experiment File Path"] == r"C:\foo.xpt"
assert plate.metadata["Protocol File Path"] == r"C:\bar.prt"
assert plate.metadata["Plate Number"] == "Plate 1"
assert plate.metadata["Reader Type"] == "Synergy H1"
assert plate.metadata["Reader Serial Number"] == "14112519"
assert plate.metadata["Reading Type"] == "Reader"
assert plate.rows == list("ABCDEFGH")
assert plate.cols == list(range(1, 13))
assert data[0].metadata["procedure"] == "foo\nbar\nquz"
assert data[1].metadata["procedure"] == "foo\tbar\nquz"
assert data[0].temperature_range == (23.8, 23.8)
assert data[1].temperature_range == (23.9, 23.9)
assert data[0].metadata["datetime"] == datetime(2019, 12, 8, 16, 22, 44)
assert data[1].metadata["datetime"] == datetime(2019, 12, 8, 16, 31, 10)
assert data[0].channels == ["YFP:485,530", "CFP:360/40,460/40"]
assert data[1].channels == ["YFP:485,530", "CFP:425,475"]
assert data[0].gains == {}
assert data[1].gains["YFP:485,530"] == 134
assert data[1].gains["CFP:425,475"] == 74
assert data[0]["G3", "YFP:485,530"] == 553
assert data[1]["G3", "CFP:425,475"] == 1566
assert np.isnan(data[1]["G11", "YFP:485,530"])
def test_time_series(filename):
data = SynergyFile(path.join("single_measurement", filename))
assert len(data) == 1
plate = data[0]
assert plate.metadata["Software Version"] == (3, 2, 1)
assert plate.metadata["Experiment File Path"] == r"C:\foo.xpt"
assert plate.metadata["Protocol File Path"] == r"C:\bar.prt"
assert plate.metadata["Plate Number"] == "Plate 1"
assert plate.metadata["Reader Type"] == "Synergy H1"
assert plate.metadata["Reader Serial Number"] == "18092726"
assert plate.metadata["Reading Type"] == "Reader"
assert plate.metadata["procedure"] == "foo\nbar\nquz"
assert plate.temperature_range == (30.0, 30.1)
assert plate.metadata["datetime"] == datetime(2020, 7, 24, 15, 55, 48)
assert plate.channels == ["Abs:600", "Abs:700", "Fluo:485,528"]
assert plate.rows == list("ABCDEFGH")
assert plate.cols == list(range(1, 13))
assert plate["B5", "Abs:600"] == 0.101
assert plate["D6", "Abs:700"] == 0.097
assert plate["G11", "Fluo:485,528"] == 104
def test_time_series(filename, temperature_ts):
data = SynergyFile(path.join("time_series", filename))
assert len(data) == 1
plate = data[0]
assert plate.metadata["Software Version"] == (3, 2, 1)
assert plate.metadata["Experiment File Path"] == r"C:\foo.xpt"
assert plate.metadata["Protocol File Path"] == r"C:\bar.prt"
assert plate.metadata["Plate Number"] == "Plate 1"
assert plate.metadata["Reader Type"] == "Synergy H1"
assert plate.metadata["Reader Serial Number"] == "18092726"
assert plate.metadata["Reading Type"] == "Reader"
assert plate.metadata["procedure"] == "foo\nbar\nquz"
assert plate.metadata["datetime"] == datetime(2020, 7, 23, 17, 40, 7)
assert plate.channels == ["OD:600"]
assert plate.rows == list("ABCDEFGH")
assert plate.cols == list(range(1, 13))
times = plate.times["OD:600"]
assert times[0] == 9 * 60 + 10
assert times[-1] == 17 * 3600 + 29 * 60 + 10
assert np.all(np.diff(times) == 10 * 60)
if temperature_ts:
temps = plate.temperatures["OD:600"]
assert len(times) == len(temps)
assert temps[0] == 30.0
assert temps[-1] == 30.1
assert temps[5] == 30.1
assert plate.temperature_range == (30.0, 30.1)
else:
assert plate.temperature_range == (0.0, 30.1)
assert plate["C12", "OD:600"][2] == 0.088
assert plate["C", 12, "OD:600"][2] == 0.088
assert plate["C", 12][2] == 0.088
assert plate["C12"][2] == 0.088
assert plate["c12", "OD:600"][2] == 0.088
assert plate["A1"][0] == 0.093
assert plate["H12"][-1] == 0.099
assert plate.results["Max V"]["D", 2, "OD:600"] == -0.060
assert plate.results["t at Max V"]["H11", "OD:600"] == 5050
assert plate.results["t at Max V"]["H11"] == 5050
def test_multiple_observables(filename, temperature_ts, separator):
data = SynergyFile(path.join("multiple_observables", filename), separator)
assert len(data) == 1
plate = data[0]
assert plate.metadata["Software Version"] == (3, 2, 1)
assert plate.metadata["Experiment File Path"] == r"C:\foo.xpt"
assert plate.metadata["Protocol File Path"] == r"C:\bar.prt"
assert plate.metadata["Plate Number"] == "Plate 1"
assert plate.metadata["Reader Type"] == "Synergy H1"
assert plate.metadata["Reader Serial Number"] == "18092726"
assert plate.metadata["Reading Type"] == "Reader"
assert plate.metadata["procedure"] == "foo\tbar\nquz"
assert plate.metadata["datetime"] == datetime(2020, 7, 24, 15, 27, 56)
assert plate.channels == ["OD:600", "485,528", "530,580"]
assert plate.rows == list("ABCDEFGH")
assert plate.cols == list(range(1, 13))
for channel, offset in [("OD:600", 108), ("485,528", 159),
("530,580", 228)]:
times = plate.times[channel]
assert times[0] == offset
assert times[-1] == offset + 20 * 60
assert np.all(np.diff(times) == 5 * 60)
if temperature_ts:
for channel in plate.channels:
temps = plate.temperatures[channel]
assert len(plate.times[channel]) == len(temps)
assert all(temp == 30.0 for temp in temps)
assert plate.temperature_range == (30.0, 30.0)
assert plate["B12", "485,528"][2] == 48
assert plate["B", 12, "485,528"][2] == 48
assert plate["b12", "485,528"][2] == 48
assert plate["H", 12, "530,580"][4] == 28
assert plate["C", 2, "OD:600"][4] == 0.085
The remaining arguments are hopefully self-explanatory and also explained in the documentation of `plot`. `fig` is a Matplotlib figure object with all the functionality that comes with that. For example, we can use `savefig` to export our plot to a file:
.. literalinclude:: ../examples/example.py
:start-after: example-st\u0061rt
:dedent: 1
:lines: 31
And this is what our plot looks like:
.. plot:: ../examples/example.py
"""
if __name__ == "__main__":
# example-start
from synergy_file_reader import SynergyFile
my_file = SynergyFile("example_data.txt")
my_plate = my_file[0]
my_plate = SynergyFile("example_data.txt")[0]
print(my_plate.channels) # ['OD:600']
channel = my_plate.channels[0]
print(channel) # 'OD:600'
print(my_plate.times[channel])
print(my_plate.temperatures[channel])
print(my_plate.metadata["Software Version"])
print(my_plate["C3", channel])
print(my_plate["c3", channel])
print(my_plate["C", 3, channel])
print(my_plate["C3"])
from synergy_file_reader import SynergyFile
import numpy as np
from matplotlib.pyplot import subplots
my_plate = SynergyFile("example_data.txt")[0]
baseline = np.percentile([ts[0] for ts in my_plate.data.values()], 10)
channel = "OD:600"
fig, axess = subplots(len(my_plate.rows),
len(my_plate.cols),
figsize=(15, 10),
sharex="all",
sharey="all")
for axess_row, row in zip(axess, my_plate.rows):
for axes, col in zip(axess_row, my_plate.cols):
axes.plot(
my_plate.times[channel] / 3600,
my_plate[row, col] - baseline,
)
axes.set_yscale("log")
axes.set_xlim(0, 10)
axes.set_ylim(1e-3, 2)
for axes, col in zip(axess[-1], my_plate.cols):
axes.set_xlabel("hours")
for axes, row in zip(axess[:, 0], my_plate.rows):
axes.set_ylabel(channel)