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added new reader
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@haeussma
haeussma committed Oct 4, 2024
1 parent 4d804fa commit c1f98dc
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Showing 11 changed files with 307 additions and 135 deletions.
Binary file added docs/examples/data/new_device_calib.xlsx
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225 changes: 93 additions & 132 deletions mtphandler/plate_manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -497,6 +497,56 @@ def _assign_species_to_all_except(
f" {init_conc} {conc_unit} to all wells except {well_ids}."
)

def create_assignment_spreadsheet(
self,
path: str = "assignment.xlsx",
):
"""Create an Excel spreadsheet for assigning initial concentrations. The spreadsheet
contains a separate sheet for each species defined on the plate, with validation
to allow only numerical values in the input cells and prevent changes to all other cells.
"""

with pd.ExcelWriter(path, engine="xlsxwriter") as writer:
df = pd.DataFrame(
index=[chr(65 + i) for i in range(8)],
columns=[str(i + 1) for i in range(12)],
)
df.to_excel(writer, sheet_name="pH", index=True)
worksheet = writer.sheets["pH"]

worksheet.data_validation(
"B2:M9",
{
"validate": "decimal",
"criteria": "between",
"minimum": 0,
"maximum": 12,
"error_message": "pH must be a numerical value between 0 and 12",
},
)
for species in self.molecules + self.proteins:
df = pd.DataFrame(
index=[chr(65 + i) for i in range(8)],
columns=[str(i + 1) for i in range(12)],
)

df.to_excel(writer, sheet_name=species.id, index=True)

worksheet = writer.sheets[species.id]

worksheet.data_validation(
"B2:M9",
{
"validate": "decimal",
"criteria": "between",
"minimum": 0,
"maximum": 1e18,
"error_message": "This cell only accepts numerical values",
},
)

print(f"Created assignment spreadsheet at {path}.")

def assign_init_conditions_from_spreadsheet(
self,
conc_unit: UnitDefinition,
Expand Down Expand Up @@ -1115,6 +1165,43 @@ def read_tekan_magellan(

return cls(**data)

@classmethod
def read_new_device(
cls,
path: str,
temperature: float,
ph: float | None = None,
name: str | None = None,
temperature_unit: UnitDefinition = C,
) -> PlateManager:
"""Read a `*.xlsx` file exported from a new device and create a PlateManager object.
Args:
path (str): Path to the file.
temperature (float): The temperature of the measurements.
ph (float | None, optional): The pH value of the measurements. Defaults to None.
name (str | None, optional): Name of the plate. Defaults to None.
temperature_unit (UnitDefinition, optional): Unit of temperature. Defaults to C.
Returns:
PlateManager: PlateManager object.
"""
from mtphandler.readers import read_new_device as reader

data: dict[str, Any] = {
"plate": reader(
path=path,
temperature=[temperature],
temperature_unit=temperature_unit,
ph=ph,
)
}

if name is not None:
data["name"] = name

return cls(**data)

@classmethod
def read_multiskan_sky(
cls,
Expand Down Expand Up @@ -1143,137 +1230,11 @@ def read_multiskan_sky(


if __name__ == "__main__":
# path = (
# "/Users/max/Documents/GitHub/MTPHandler/docs/examples/data/spectra_max_190.txt"
# )

# pm = PlateManager.read_spectra_max_190(path, ph=6.9)
# pm.visualize()

# pm

# h1 = pm.get_well("H1")

# print(h1.id)
# print(h1.x_pos)
# print(h1.y_pos)
# print(h1.measurements[0].absorption[0])
# print(h1.measurements[0].absorption[-1])

# path = "/Users/max/Documents/GitHub/MTPHandler/docs/examples/data/tekan_spark.xlsx"
# from mtphandler.model import Plate

# p = PlateManager.read_tecan_spark(path, 7.4)

# print(p.plate.temperatures)

# p.visualize()

# path = "/Users/max/Documents/GitHub/MTPHandler/docs/examples/data/magellan.xlsx"

# plate = PlateManager.read_tekan_magellan(path, wavelength=600, ph=7)

# plate.visualize()

# path = (
# "/Users/max/Documents/training_course/jules/Spectramax190 molecular Devices.txt"
# )

# from mtphandler.units import mM

# pm = PlateManager.read_spectra_max_190(path, ph=7)
# # pm.visualize()
# testo = pm.define_molecule("testo", 60857, "testosterone")
# mpi = pm.define_molecule("mpi", 60961, "methylparaben")

# pm.assign_species(
# species=testo,
# init_conc=0.1,
# conc_unit=mM,
# to="all",
# )

# path = (
# "/Users/max/Documents/GitHub/MTPHandler/docs/examples/data/ BioTek_Epoch2.xlsx"
# )

# from mtphandler.units import mM

# p = PlateManager.read_biotek(path, ph=7.4)
# p.visualize()

# testo = p.define_molecule("testo", 60857, "testosterone")
# aldolase = p.define_protein("aldolase", "Aldolase")
path = "docs/examples/data/ BioTek_Epoch2.xlsx"

# p.assign_init_conditions(
# species=testo,
# init_conc=0.1,
# conc_unit=mM,
# to="all",
# )
p = PlateManager.read_biotek(path)
p.define_molecule("alc", 123)
p.define_molecule("ala", 124)
p.define_protein("asd", "adfaddf")

# aldo = p.define_protein("aldolase", "Aldolase")
# p.assign_init_conditions(
# species=aldo, init_conc=0.1, conc_unit=mM, to="all", contributes_to_signal=False
# )

# enz = p.to_enzymeml(name="Test EnzymeML", wells_with_protein_only=False)

# with open("enz.json", "w") as f:
# f.write(enz.model_dump_json(indent=4))
# print(len(enz.measurements))

# from mtphandler.units import C, min

# path = "docs/examples/data/multiskan_spectrum_1500.txt"

# ph = 7.0
# wavelength = 450.0

# time = np.arange(0, 15.5, 0.5).tolist()
# print(f"the thime is {time}")

# plate = PlateManager.read_multiskan_spectrum_1500(
# path=path,
# ph=ph,
# time=time,
# time_unit=min,
# temperature=37.0,
# temperature_unit=C,
# )
# plate.visualize()

path = (
"/Users/max/Documents/GitHub/MTPHandler/docs/examples/data/Multiskan Sky.xlsx"
)

p = PlateManager.read_multiskan_sky(path, ph=None)
p.visualize(darkmode=True)
print(p)


class BlankResult(BaseModel):
species_id: str = Field(
description="The id of the species for which the blank was calculated.",
default=None,
)
wavelength: float = Field(
description="The wavelength at which the blank was calculated.",
default=None,
)
control_well_ids: list[str] = Field(
description="The ids of the wells used to calculate the blank.",
default=[],
)
mean_contribution: float = Field(
description="The mean contribution of the species to the signal.",
default=None,
)
std_contribution: float = Field(
description="The standard deviation of the contribution of the species to the signal.",
default=None,
)
applied_to_well_ids: list[str] = Field(
description="The ids of the wells to which the blank was applied.",
default=[],
)
p.create_assignment_spreadsheet()
1 change: 1 addition & 0 deletions mtphandler/readers/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,4 @@
from .tekan_magellan import read_tekan_magellan # noqa
from .tekan_spark import read_tekan_spark # noqa
from .multiskan_sky import read_multiskan_sky # noqa
from .new_device import read_new_device # noqa
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